0.1 Импорт

Импорт phyloseq объекта и библиотек
Датасет - хроносерия разложения соломы - от фактор Day 10ти уровней

library(phyloseq)
library(tidyverse)
library(ggpubr)
library(ampvis2)
library(ANCOMBC)
library(heatmaply)
library(compositions)
library(igraph)
library(WGCNA)
require(DESeq2)
require(phyloseq)

ps.f <- readRDS("psf2")

0.2 functions

#phyloseq object to ampvis2 object
#https://gist.github.com/KasperSkytte/8d0ca4206a66be7ff6d76fc4ab8e66c6

phyloseq_to_ampvis2 <- function(physeq) {
  #check object for class
  if(!any(class(physeq) %in% "phyloseq"))
    stop("physeq object must be of class \"phyloseq\"", call. = FALSE)
  
  #ampvis2 requires taxonomy and abundance table, phyloseq checks for the latter
  if(is.null(physeq@tax_table))
    stop("No taxonomy found in the phyloseq object and is required for ampvis2", call. = FALSE)
  
  #OTUs must be in rows, not columns
  if(phyloseq::taxa_are_rows(physeq))
    abund <- as.data.frame(phyloseq::otu_table(physeq)@.Data)
  else
    abund <- as.data.frame(t(phyloseq::otu_table(physeq)@.Data))
  
  #tax_table is assumed to have OTUs in rows too
  tax <- phyloseq::tax_table(physeq)@.Data
  
  #merge by rownames (OTUs)
  otutable <- merge(
    abund,
    tax,
    by = 0,
    all.x = TRUE,
    all.y = FALSE,
    sort = FALSE
  )
  colnames(otutable)[1] <- "OTU"
  
  #extract sample_data (metadata)
  if(!is.null(physeq@sam_data)) {
    metadata <- data.frame(
      phyloseq::sample_data(physeq),
      row.names = phyloseq::sample_names(physeq), 
      stringsAsFactors = FALSE, 
      check.names = FALSE
    )
    
    #check if any columns match exactly with rownames
    #if none matched assume row names are sample identifiers
    samplesCol <- unlist(lapply(metadata, function(x) {
      identical(x, rownames(metadata))}))
    
    if(any(samplesCol)) {
      #error if a column matched and it's not the first
      if(!samplesCol[[1]])
        stop("Sample ID's must be in the first column in the sample metadata, please reorder", call. = FALSE)
    } else {
      #assume rownames are sample identifiers, merge at the end with name "SampleID"
      if(any(colnames(metadata) %in% "SampleID"))
        stop("A column in the sample metadata is already named \"SampleID\" but does not seem to contain sample ID's", call. = FALSE)
      metadata$SampleID <- rownames(metadata)
      
      #reorder columns so SampleID is the first
      metadata <- metadata[, c(which(colnames(metadata) %in% "SampleID"), 1:(ncol(metadata)-1L)), drop = FALSE]
    }
  } else
    metadata <- NULL
  
  #extract phylogenetic tree, assumed to be of class "phylo"
  if(!is.null(physeq@phy_tree)) {
    tree <- phyloseq::phy_tree(physeq)
  } else
    tree <- NULL
  
  #extract OTU DNA sequences, assumed to be of class "XStringSet"
  if(!is.null(physeq@refseq)) {
    #convert XStringSet to DNAbin using a temporary file (easiest)
    fastaTempFile <- tempfile(pattern = "ampvis2_", fileext = ".fa")
    Biostrings::writeXStringSet(physeq@refseq, filepath = fastaTempFile)
  } else
    fastaTempFile <- NULL
  
  #load as normally with amp_load
  ampvis2::amp_load(
    otutable = otutable,
    metadata = metadata,
    tree = tree,
    fasta = fastaTempFile
  )
}

#variance stabilisation from DESeq2

ps_vst <- function(ps, factor){
  

  
  diagdds = phyloseq_to_deseq2(ps, as.formula(paste( "~", factor)))              
  diagdds = estimateSizeFactors(diagdds, type="poscounts")
  diagdds = estimateDispersions(diagdds, fitType = "local") 
  pst <- varianceStabilizingTransformation(diagdds)
  pst.dimmed <- t(as.matrix(assay(pst))) 
  # pst.dimmed[pst.dimmed < 0.0] <- 0.0
  ps.varstab <- ps
  otu_table(ps.varstab) <- otu_table(pst.dimmed, taxa_are_rows = FALSE) 
  return(ps.varstab)
}

#WGCNA visualisation
#result - list class object with attributes:
# ps - phyloseq object
# amp - ampwis2 object
# heat - heatmap with absalute read numbers
# heat_rel - hetmap with relative abundances
# tree - phylogenetic tree with taxonomy

color_filt <- function(ps, df){
  
      library(tidyverse)
      library(reshape2)
      library(gridExtra)

  
  l = list()
  for (i in levels(df$module)){
    message(i)
    color_name <-  df %>% 
      filter(module == i) %>% 
      pull(asv) %>% 
      unique()
    ps.col <- prune_taxa(color_name, ps)
    amp.col <- phyloseq_to_ampvis2(ps.col)
    heat <- amp_heatmap(amp.col, tax_show = 60, 
              group_by = "Day", 
              tax_aggregate = "OTU",
              tax_add = "Genus", 
              normalise=FALSE, 
              showRemainingTaxa = TRUE)
    
    ps.rel  <-  phyloseq::transform_sample_counts(ps.col, function(x) x / sum(x) * 100)
    amp.r <- phyloseq_to_ampvis2(ps.rel)
    heat.rel <- amp_heatmap(amp.r, tax_show = 60, 
          group_by = "Day", 
          tax_aggregate = "OTU",
          tax_add = "Genus", 
          normalise=FALSE, 
          showRemainingTaxa = TRUE)
    
    tree <- ps.col@phy_tree
    taxa <- as.data.frame(ps.col@tax_table@.Data)
    p1 <- ggtree(tree) + 
              geom_tiplab(size=2, align=TRUE, linesize=.5) +
              theme_tree2()
    
    taxa[taxa == "Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium"] <- "Allorhizobium"
    taxa[taxa == "Burkholderia-Caballeronia-Paraburkholderia"] <- "Burkholderia"
  
    tx <- taxa %>% 
      rownames_to_column("id") %>% 
      mutate(id = factor(id, levels = rev(get_taxa_name(p1)))) %>% 
      dplyr::select(-c(Kingdom, Species, Order)) %>% 
      melt(id.var = 'id')

    p2 <- ggplot(tx, aes(variable, id)) + 
      geom_tile(aes(fill = value), alpha = 0.4) +
      geom_text(aes(label = value), size = 3) +
      theme_bw() + 
      theme(legend.position = "none",
             axis.ticks.x=element_blank(),
             axis.text.y=element_blank(),
             axis.ticks.y=element_blank(),
             axis.title.x = element_blank(),
            axis.title.y = element_blank()) 

    p <- ggpubr::ggarrange(p1, p2, widths = c(0.9, 1))
    l[[i]] <- list("ps" = ps.col, 
                   "amp" = amp.col,
                   "heat" = heat,
                   "heat_rel" = heat.rel,
                   "tree" = p,
                   "taxa" = knitr::kable(taxa))
                    
  }
  return(l)
}


color_filt_broken <- function(ps, df, ps.pruned){
  
      library(tidyverse)
      library(reshape2)
      library(gridExtra)

  
  l = list()
  for (i in levels(df$module)){
    message(i)
    color_name <-  df %>% 
      filter(module == i) %>% 
      pull(asv) %>% 
      unique()
    ps.col <- prune_taxa(color_name, ps)
    ps.col.pruned <- prune_taxa(color_name, ps.pruned)
    amp.col <- phyloseq_to_ampvis2(ps.col)
    heat <- amp_heatmap(amp.col, tax_show = 60, 
              group_by = "Day", 
              tax_aggregate = "OTU",
              tax_add = "Genus", 
              normalise=FALSE, 
              showRemainingTaxa = TRUE)
    
    ps.rel  <-  phyloseq::transform_sample_counts(ps.col, function(x) x / sum(x) * 100)
    amp.r <- phyloseq_to_ampvis2(ps.rel)
    heat.rel <- amp_heatmap(amp.r, tax_show = 60, 
          group_by = "Day", 
          tax_aggregate = "OTU",
          tax_add = "Genus", 
          normalise=FALSE, 
          showRemainingTaxa = TRUE)
    
    tree <- ps.col.pruned@phy_tree
    taxa <- as.data.frame(ps.col.pruned@tax_table@.Data)
    p1 <- ggtree(tree) + 
              geom_tiplab(size=2, align=TRUE, linesize=.5) +
              theme_tree2()
    
    taxa[taxa == "Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium"] <- "Allorhizobium"
    taxa[taxa == "Burkholderia-Caballeronia-Paraburkholderia"] <- "Burkholderia"
  
    tx <- taxa %>% 
      rownames_to_column("id") %>% 
      mutate(id = factor(id, levels = rev(get_taxa_name(p1)))) %>% 
      dplyr::select(-c(Kingdom, Species, Order)) %>% 
      melt(id.var = 'id')

    p2 <- ggplot(tx, aes(variable, id)) + 
      geom_tile(aes(fill = value), alpha = 0.4) +
      geom_text(aes(label = value), size = 3) +
      theme_bw() + 
      theme(legend.position = "none",
             axis.ticks.x=element_blank(),
             axis.text.y=element_blank(),
             axis.ticks.y=element_blank(),
             axis.title.x = element_blank(),
            axis.title.y = element_blank()) 

    p <- ggpubr::ggarrange(p1, p2, widths = c(0.9, 1))
    l[[i]] <- list("ps" = ps.col, 
                   "amp" = amp.col,
                   "heat" = heat,
                   "heat_rel" = heat.rel,
                   "tree" = p,
                   "taxa" = knitr::kable(taxa))
                    
  }
  return(l)
}

detachAllPackages <- function() {

  basic.packages <- c("package:stats","package:graphics","package:grDevices","package:utils","package:datasets","package:methods","package:base")

  package.list <- search()[ifelse(unlist(gregexpr("package:",search()))==1,TRUE,FALSE)]

  package.list <- setdiff(package.list,basic.packages)

  if (length(package.list)>0)  for (package in package.list) detach(package, character.only=TRUE, force = TRUE)

}

plot_alpha_w_toc <- function(ps, group, metric) {
  
  require(phyloseq)
  require(ggplot2)
  
  ps_a <- prune_taxa(taxa_sums(ps) > 0, ps)
  
  er <- estimate_richness(ps_a)
  df_er <- cbind(ps_a@sam_data, er)
  df_er <- df_er %>% select(c(group, metric))
  stat.test <- aov(as.formula(paste0(metric, "~", group)), data = df_er) %>%
    rstatix::tukey_hsd()
  y <-  seq(max(er[[metric]]), length=length(stat.test$p.adj), by=max(er[[metric]]/20))

  plot_richness(ps_a, x=group, measures=metric) + 
    geom_boxplot() +
    geom_point(size=1.2, alpha=0.3) +
    ggpubr::stat_pvalue_manual(
      stat.test, 
      label = "p.adj.signif", 
      y.position = y) +
    theme_light() + 
    scale_color_brewer(palette="Dark2") +
    theme(axis.text.x = element_text(angle = 90),
          axis.title.x=element_blank()) +
    labs(y=paste(metric, "index")) 
}


# standart NMDS plot tool frop phyloseq with some additional aestatics 
# have stress value on plot - may work as fuck
beta_custom_norm_NMDS_elli_w <- function(ps, seed = 7888, normtype="vst", Color="What", Group="Repeat"){
  require(phyloseq)
  require(ggplot2)
  require(ggpubr)
  library(ggforce)
  
  
  ordination.b <- ordinate(ps, "NMDS", "bray")
  mds <- as.data.frame(ordination.b$points)
  p  <-  plot_ordination(ps,
                         ordination.b,
                         type="sample",
                         color = Color,
                         title="NMDS - Bray-Curtis",
                         # title=NULL,
                         axes = c(1,2) ) + 
    theme_bw() + 
    theme(text = element_text(size = 10)) + 
    geom_point(size = 3) +
    annotate("text",
    x=min(mds$MDS1) + abs(min(mds$MDS1))/7,
    y=max(mds$MDS2),
    label=paste0("Stress -- ", round(ordination.b$stress, 3))) +
    geom_mark_ellipse(aes_string(group = Group, label = Group),
                      label.fontsize = 10,
                      label.buffer = unit(2, "mm"),
                      label.minwidth = unit(5, "mm"),
                      con.cap = unit(0.1, "mm"),
                      con.colour='gray') +
    theme(legend.position = "none") +
    ggplot2::scale_fill_viridis_c(option = "H")
  
  return(p)
}


# alpha with aov + tukie post-hock - useless, but it looks pretty good
plot_alpha_w_toc <- function(ps, group, metric) {
  
  require(phyloseq)
  require(ggplot2)
  
  ps_a <- prune_taxa(taxa_sums(ps) > 0, ps)
  
  er <- estimate_richness(ps_a)
  df_er <- cbind(ps_a@sam_data, er)
  df_er <- df_er %>% select(c(group, metric))
  stat.test <- aov(as.formula(paste0(metric, "~", group)), data = df_er) %>%
    rstatix::tukey_hsd()
  y <- seq(max(er[[metric]]), length=length(stat.test$p.adj.signif[stat.test$p.adj.signif != "ns"]), by=max(er[[metric]]/20))
  
  plot_richness(ps_a, x=group, measures=metric) + 
    geom_boxplot() +
    geom_point(size=1.2, alpha=0.3) +
    stat_pvalue_manual(
      stat.test, 
      label = "p.adj.signif", 
      y.position = y,
      hide.ns=TRUE) +
    theme_light() + 
    scale_color_brewer(palette="Dark2") +
    theme(axis.text.x = element_text(angle = 90),
          axis.title.x=element_blank()) +
    labs(y=paste(metric, "index")) 
}

0.3 Alpha

p1 <- plot_alpha_w_toc(ps = ps.f, group = "Day", metric = "Observed")
p2 <- plot_alpha_w_toc(ps = ps.f, group = "Day", metric = "Shannon")
p3 <- plot_alpha_w_toc(ps = ps.f, group = "Day", metric = "InvSimpson")
ggarrange(p1, p2, p3, nrow = 1)


Add Group parameter to metadata -
- early - D01, D03, D05
- middle - D07, D08, D10
- late - D13, D14, D15

sample.data <- ps.f@sam_data %>% 
  data.frame() %>% 
  mutate(Group = if_else(Day %in% c("D01", "D03", "D05"), "early", 
                         if_else(Day %in% c("D07", "D08","D10"), "middle", "late"))) %>% 
  mutate(Group = factor(Group, levels=c("early", "middle","late"))) %>% 
  phyloseq::sample_data()

sample_data(ps.f) <- sample.data

p.observed <- plot_alpha_w_toc(ps = ps.f, group = "Group", metric = c("Observed")) + 
  theme(axis.title.y = element_blank())

p.shannon <- plot_alpha_w_toc(ps = ps.f, group = "Group", metric = c("Shannon")) + 
  theme(axis.title.y = element_blank())

p.simpson <- plot_alpha_w_toc(ps = ps.f, group = "Group", metric = c("InvSimpson")) + 
  theme(axis.title.y = element_blank())

ggpubr::ggarrange(p.observed, p.shannon, p.simpson, ncol = 3)

0.4 beta statistic

0.4.1 permanova

permanova - group significantlly different - dispersion between is more, than inside groups

dist <- phyloseq::distance(ps.f, "bray")
metadata <- as(sample_data(ps.f@sam_data), "data.frame")
vegan::adonis2(dist ~ Group, data = metadata)
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
## 
## vegan::adonis2(formula = dist ~ Group, data = metadata)
##          Df SumOfSqs      R2      F Pr(>F)    
## Group     2   3.2742 0.33893 8.2033  0.001 ***
## Residual 32   6.3861 0.66107                  
## Total    34   9.6604 1.00000                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

0.4.2 dynamic of beta diversity

Дистанция брей кертиса по шагам между каждыми днями.   (Например - все D15 против D14)   Может на эту картинку подвесить еще почвенное дыхание?

ps.f.r <- rarefy_even_depth(ps.f, rngseed = 777)

avg.r <- ps.f.r@otu_table %>% 
  as.data.frame() %>%
  vegan::avgdist(10)

avg <- ps.f@otu_table %>% 
  as.data.frame() %>%
  vegan::avgdist(10)

# avg %>%
#   as.matrix() %>%
#   as_tibble(rownames= "sample") %>%
#   pivot_longer(-sample) %>%
#   filter(sample < name) %>%
#   mutate(repeat_a = str_replace(sample, ".*-", ""),
#          repeat_b = str_replace(name, ".*-", ""), 
#          day_a = as.numeric(str_replace(sapply(strsplit(sample, "-"), `[`, 3), "D", "")),
#           day_b = as.numeric(str_replace(sapply(strsplit(name, "-"), `[`, 3), "D", "")),
#          diff = abs(day_a - day_b),
#          early = day_a < 10) %>% 
#   filter(repeat_a == repeat_b & diff < 10) %>%
#   group_by(diff, repeat_a, early) %>%
#   summarize(median = median(value)) %>%
#   ungroup() %>%
#   ggplot(aes(x=diff, y=median, color=early, group=paste0(repeat_a, early))) +
#   geom_line(size=0.25) +
#   geom_smooth(aes(group=early), se=FALSE, size=4) +
#   labs(x="Distance between time points",
#        y="Median Bray-Curtis distance") +
#   scale_x_continuous(breaks=1:9) +
#   scale_color_manual(name=NULL,
#                      breaks=c(TRUE, FALSE),
#                      values=c("blue", "red"),
#                      labels=c("Early", "Late")) +
#   guides(color = guide_legend(override.aes = list(size=1))) +
#   theme_classic()

avg.r %>%
  as.matrix() %>%
  as_tibble(rownames= "sample") %>%
  pivot_longer(-sample) %>%
  filter(sample < name) %>%
  mutate(repeat_a = str_replace(sample, ".*-", ""),
         repeat_b = str_replace(name, ".*-", ""), 
         day_a = as.numeric(str_replace(sapply(strsplit(sample, "-"), `[`, 3), "D", "")),
          day_b = as.numeric(str_replace(sapply(strsplit(name, "-"), `[`, 3), "D", ""))) %>% 
  mutate(day_a = as.numeric(as.factor(day_a) %>% forcats::fct_recode("2" = "3", "3" = "5", "4" = "7", "5" = "8", "6" = "10", "7" = "13", "8" = "14", "9" = "14", "10" = "15")),
         day_b = as.numeric(as.factor(day_b) %>% forcats::fct_recode("2" = "3", "3" = "5", "4" = "7", "5" = "8", "6" = "10", "7" = "12", "8" = "13", "9" = "14", "10" = "15")),
         diff = abs(day_a - day_b)) %>% 
  filter(diff == 1) %>% 
  mutate(day_b = as.factor(day_b) %>% forcats::fct_recode("D03" = "2", "D05" = "3","D07" = "4",  "D08" = "5", "D10" = "6", "D13" = "7", "D14" = "8", "D15" = "10", "D12" = "7")) %>% 
  ggplot(aes(x=day_b, y=value)) +
    geom_boxplot() +
  theme_bw() +
  labs(x="Time points",
       y="Bray-Curtis distance")

0.4.3 basic NMDS plot

По картинке кажется что происходит постепенное замедление изменений -
но из предыдущей картинки следует, что это не так - есть провал между 7-8-10,
но в среднем точки различаются довольно одинакого.

beta_custom_norm_NMDS_elli_w(ps.f, C="Group", G="Day")
## Square root transformation
## Wisconsin double standardization
## Run 0 stress 0.1048129 
## Run 1 stress 0.1372731 
## Run 2 stress 0.1318495 
## Run 3 stress 0.1048129 
## ... Procrustes: rmse 0.00004856956  max resid 0.0001949092 
## ... Similar to previous best
## Run 4 stress 0.1048129 
## ... New best solution
## ... Procrustes: rmse 0.00001842645  max resid 0.00006948497 
## ... Similar to previous best
## Run 5 stress 0.1426236 
## Run 6 stress 0.1048204 
## ... Procrustes: rmse 0.001770292  max resid 0.007527799 
## ... Similar to previous best
## Run 7 stress 0.1064532 
## Run 8 stress 0.1064733 
## Run 9 stress 0.1048204 
## ... Procrustes: rmse 0.001767644  max resid 0.007510715 
## ... Similar to previous best
## Run 10 stress 0.1064532 
## Run 11 stress 0.1318495 
## Run 12 stress 0.1064733 
## Run 13 stress 0.1064733 
## Run 14 stress 0.1460032 
## Run 15 stress 0.1048204 
## ... Procrustes: rmse 0.001769848  max resid 0.007525048 
## ... Similar to previous best
## Run 16 stress 0.1064532 
## Run 17 stress 0.1372728 
## Run 18 stress 0.1048129 
## ... Procrustes: rmse 0.000002711789  max resid 0.0000100797 
## ... Similar to previous best
## Run 19 stress 0.1460029 
## Run 20 stress 0.146003 
## *** Solution reached

0.5 Splitting the dataset

Разделим датасет на две группы

1-я - в более чем 10% образцов должно быть хотя бы 10 ридов - эта группа пойдет в анализ далее

ps.inall <- phyloseq::filter_taxa(ps.f, function(x) sum(x > 10) > (0.1*length(x)), TRUE)

amp.inall <- phyloseq_to_ampvis2(ps.inall)
amp_heatmap(amp.inall,
            tax_show = 40,
            group_by = "Day",
            tax_aggregate = "OTU",
            tax_add = "Genus",
            normalise=FALSE,
            showRemainingTaxa = TRUE)

Вторая - оставшиеся, но более 100 ридов по всем образцам(далее - вылетающие мажоры(ВМ))
Остальные филотипы выкидываем из анализа

ps.exl  <- phyloseq::filter_taxa(ps.f, function(x) sum(x > 10) < (0.1*length(x)), TRUE)
ps.exl  <- prune_taxa(taxa_sums(ps.exl) > 100, ps.exl)
amp.exl <- phyloseq_to_ampvis2(ps.exl)
amp_heatmap(amp.exl,
            tax_show = 40,
            group_by = "Day",
            tax_aggregate = "OTU",
            tax_add = "Genus",
            normalise=FALSE,
            showRemainingTaxa = TRUE)

То же, но c относительной представленностью.

ps.per  <-  phyloseq::transform_sample_counts(ps.f, function(x) x / sum(x) * 100) 
ps.exl.taxa <- taxa_names(ps.exl)
ps.per.exl <- prune_taxa(ps.exl.taxa, ps.per)
amp.exl.r <- phyloseq_to_ampvis2(ps.per.exl)

amp_heatmap(amp.exl.r, tax_show = 60, 
      group_by = "Day", 
      tax_aggregate = "OTU",
      tax_add = "Genus", 
      round =  2, 
      normalise=FALSE, 
      showRemainingTaxa = TRUE)

amp_heatmap(amp.exl.r, tax_show = 60, 
      group_by = "Day", 
      tax_aggregate = "OTU",
      tax_add = "Genus", 
      round =  2, 
      normalise=FALSE, )

ВМ объединенные по родам. Относительная представленность.

amp_heatmap(amp.exl.r,
            tax_show = 30, 
            group_by = "Day", 
            tax_aggregate = "Genus",
            tax_add = "Phylum",
            tax_class = "Proteobacteria",
            round =  2,
            normalise=FALSE, 
            showRemainingTaxa = TRUE)

Если посмотреть, если как распределяются ВМ по дням - похоже распределение ВМ связано не только с особенностью отдельных мешочков, но и с чисто техническими особенностями - вылетающие значения вылетают в основном не с биологическими повторностями, а с техническими(красная линия - выбрана визуально)

p_box <- phyloseq::sample_sums(ps.per.exl) %>% 
  as.data.frame(col.names = "values") %>% 
  setNames(., nm = "values") %>% 
  rownames_to_column("samples") %>% 
  mutate(Day = sapply(strsplit(samples, "-"), `[`, 3)) %>% 
  ggplot(aes(x=Day, y=values, color=Day, fill = Day)) +
  geom_boxplot(aes(color=Day, fill = Day)) +
  geom_point(color = "black", position = position_dodge(width=0.2)) +
  geom_hline(yintercept = 10, colour = "red") +
  theme_bw() +
  theme(legend.position = "none")
     
p_box <- p_box + viridis::scale_color_viridis(option = "H", discrete = TRUE, direction=1, begin=0.1, end = 0.9, alpha = 0.5)

p_box + viridis::scale_fill_viridis(option = "H", discrete = TRUE, direction=1, begin=0.1, end = 0.9, alpha = 0.3)

0.6 WGCNA

0.6.1 clr

после clr нормализации / выглядит отвратительно попробуем нормализацию vst из DESeq2

otu.inall <- as.data.frame(ps.inall@otu_table@.Data) 
ps.inall.clr <- ps.inall
otu_table(ps.inall.clr) <- phyloseq::otu_table(compositions::clr(otu.inall), taxa_are_rows = FALSE)
data <- ps.inall.clr@otu_table@.Data %>% 
  as.data.frame()
rownames(data) <- as.character(ps.inall.clr@sam_data$Description)
powers <-  c(c(1:10), seq(from = 12, to=30, by=1))
sft <-  pickSoftThreshold(data, powerVector = powers, verbose = 5, networkType = "signed")
## pickSoftThreshold: will use block size 338.
##  pickSoftThreshold: calculating connectivity for given powers...
##    ..working on genes 1 through 338 of 338
## Warning: executing %dopar% sequentially: no parallel backend registered
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
## 1      1    0.185  23.60         0.8790 168.0000 168.00000 172.000
## 2      2    0.199 -15.50         0.8970  87.6000  87.20000  95.100
## 3      3    0.518 -13.10         0.8580  47.3000  46.80000  55.900
## 4      4    0.390  -6.46         0.8050  26.5000  26.00000  34.500
## 5      5    0.262  -3.46         0.7820  15.4000  14.90000  22.300
## 6      6    0.232  -2.30         0.7770   9.2300   8.78000  15.000
## 7      7    0.251  -1.87         0.6990   5.7300   5.36000  10.500
## 8      8    0.319  -1.75         0.7570   3.6800   3.41000   7.620
## 9      9    0.527  -2.07         0.7770   2.4400   2.20000   5.890
## 10    10    0.648  -2.28         0.8490   1.6600   1.47000   4.690
## 11    12    0.827  -2.41         0.8970   0.8420   0.69300   3.190
## 12    13    0.793  -2.38         0.7930   0.6220   0.49000   2.700
## 13    14    0.277  -3.97         0.0914   0.4690   0.35500   2.320
## 14    15    0.282  -3.83         0.1000   0.3610   0.26100   2.010
## 15    16    0.894  -2.17         0.9030   0.2820   0.19800   1.770
## 16    17    0.905  -2.10         0.9080   0.2240   0.15000   1.560
## 17    18    0.922  -2.04         0.9240   0.1810   0.11500   1.390
## 18    19    0.927  -2.01         0.9230   0.1480   0.08820   1.250
## 19    20    0.938  -1.93         0.9370   0.1220   0.06780   1.130
## 20    21    0.946  -1.86         0.9470   0.1020   0.05260   1.020
## 21    22    0.315  -3.12         0.2220   0.0856   0.04140   0.926
## 22    23    0.303  -3.96         0.1560   0.0728   0.03270   0.844
## 23    24    0.307  -2.92         0.1940   0.0623   0.02590   0.772
## 24    25    0.303  -2.84         0.1800   0.0538   0.02060   0.708
## 25    26    0.921  -1.63         0.8990   0.0467   0.01650   0.657
## 26    27    0.892  -1.61         0.8650   0.0408   0.01320   0.622
## 27    28    0.155  -1.93        -0.0202   0.0359   0.01040   0.591
## 28    29    0.199  -2.77        -0.0228   0.0317   0.00841   0.563
## 29    30    0.199  -2.69        -0.0203   0.0282   0.00684   0.537
plot(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2], xlab="Soft Threshold (power)",ylab="Scale Free Topology Model Fit,signed R^2",type="n", main = paste("Scale independence"))
text(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2], labels=powers,cex=0.9,col="red")
abline(h=0.9,col="salmon")

0.6.2 vst

после vst нормализации

ps.varstab <- ps_vst(ps.inall, "Day")

data2 <- ps.varstab@otu_table@.Data %>% 
  as.data.frame()

rownames(data2) <- as.character(ps.varstab@sam_data$Description)
powers <-  c(seq(from = 1, to=10, by=0.5), seq(from = 11, to=20, by=1))
sft2 <-  pickSoftThreshold(data2, powerVector = powers, verbose = 5, networkType = "signed hybrid")
## pickSoftThreshold: will use block size 338.
##  pickSoftThreshold: calculating connectivity for given powers...
##    ..working on genes 1 through 338 of 338
##    Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1    1.0    0.409 -1.05          0.704  50.100  45.60000  97.80
## 2    1.5    0.578 -1.07          0.895  30.900  27.00000  71.20
## 3    2.0    0.723 -1.15          0.942  20.300  17.90000  53.60
## 4    2.5    0.767 -1.24          0.871  14.000  12.00000  41.70
## 5    3.0    0.809 -1.31          0.909  10.000   7.86000  33.40
## 6    3.5    0.872 -1.31          0.958   7.380   5.39000  27.30
## 7    4.0    0.888 -1.30          0.968   5.580   3.76000  22.60
## 8    4.5    0.858 -1.36          0.910   4.320   2.67000  19.00
## 9    5.0    0.892 -1.36          0.943   3.400   1.94000  16.20
## 10   5.5    0.899 -1.38          0.954   2.720   1.41000  13.90
## 11   6.0    0.896 -1.39          0.962   2.210   1.07000  12.10
## 12   6.5    0.897 -1.33          0.962   1.820   0.84700  10.60
## 13   7.0    0.910 -1.30          0.970   1.520   0.65400   9.30
## 14   7.5    0.914 -1.31          0.966   1.280   0.51500   8.25
## 15   8.0    0.913 -1.28          0.954   1.090   0.41500   7.36
## 16   8.5    0.905 -1.28          0.937   0.938   0.34000   6.59
## 17   9.0    0.895 -1.30          0.913   0.813   0.27800   5.99
## 18   9.5    0.878 -1.33          0.900   0.709   0.23200   5.49
## 19  10.0    0.886 -1.34          0.894   0.624   0.19100   5.07
## 20  11.0    0.911 -1.31          0.928   0.491   0.12500   4.35
## 21  12.0    0.890 -1.29          0.894   0.396   0.08590   3.79
## 22  13.0    0.910 -1.26          0.918   0.325   0.06120   3.33
## 23  14.0    0.882 -1.25          0.856   0.272   0.04420   2.95
## 24  15.0    0.889 -1.19          0.864   0.230   0.03230   2.63
## 25  16.0    0.913 -1.18          0.893   0.198   0.02240   2.35
## 26  17.0    0.930 -1.16          0.912   0.172   0.01620   2.20
## 27  18.0    0.955 -1.19          0.947   0.151   0.01190   2.09
## 28  19.0    0.908 -1.21          0.896   0.134   0.00896   1.99
## 29  20.0    0.916 -1.21          0.906   0.120   0.00649   1.91
plot(sft2$fitIndices[,1], -sign(sft2$fitIndices[,3])*sft2$fitIndices[,2], xlab="Soft Threshold (power)",ylab="Scale Free Topology Model Fit,signed R^2",type="n", main = paste("Scale independence"))
text(sft2$fitIndices[,1], -sign(sft2$fitIndices[,3])*sft2$fitIndices[,2], labels=powers,cex=0.9,col="red")
abline(h=0.9,col="salmon")

# WGCNA, as old and not supported
detachAllPackages()
library(WGCNA)


net3 <- WGCNA::blockwiseModules(data2,
                          power=5.5,
                          TOMType="signed",
                          networkType="signed hybrid",
                          nThreads=0)


mergedColors2 <-  WGCNA::labels2colors(net3$colors, colorSeq = c("salmon", "darkgreen", "cyan", "red", "blue", "plum"))

plotDendroAndColors(
  net3$dendrograms[[1]],
  mergedColors2[net3$blockGenes[[1]]],
  "Module colors",
  dendroLabels = FALSE,
  hang = 0.03,
  addGuide = TRUE,
  guideHang = 0.05)

0.6.2.1 Импорт 2

library(phyloseq)
library(tidyverse)
library(ggpubr)
library(ampvis2)
library(heatmaply)
library(WGCNA)
library(phyloseq)
library(ggtree)
library(tidyverse)
library(KneeArrower)
modules_of_interest = mergedColors2 %>% 
  unique()

module_df <- data.frame(
  asv = names(net3$colors),
  colors = mergedColors2
)

# module_df[module_df == "yellow"] <- "salmon"

submod <-  module_df %>%
  subset(colors %in% modules_of_interest)

row.names(module_df) = module_df$asv

subexpr = as.data.frame(t(data2))[submod$asv,]

submod_df <- data.frame(subexpr) %>%
  mutate(
    asv = row.names(.)
  ) %>%
  pivot_longer(-asv) %>%
  mutate(
    module = module_df[asv,]$colors
  )

submod_df <- submod_df %>% 
  mutate(name = gsub("\\_.*","",submod_df$name)) %>% 
  group_by(name, asv) %>% 
  summarise(value = mean(value), asv = asv, module = module) %>% 
  relocate(c(asv, name, value, module)) %>% 
  ungroup() %>% 
  mutate(module = as.factor(module))

p <- submod_df %>% 
  ggplot(., aes(x=name, y=value, group=asv)) +
  geom_line(aes(color = module),
            alpha = 0.2) +
  theme_bw() +
  theme(
    axis.text.x = element_text(angle = 90),
    legend.position = "none") +
  facet_grid(rows = vars(module)) +
  labs(x = "treatment",
       y = "normalized expression")

p + scale_color_manual(values = levels(submod_df$module))

0.6.2.2 ordination

UNIFRAC - колбаска сужается

ps.inall.col <- ps.inall
df <- module_df %>% 
  rename("id" = "asv")
df <- df %>% 
  dplyr::select(-"id") %>% 
  mutate(colors = as.factor(colors))
taxa <- as.data.frame(ps.inall@tax_table@.Data)
tx <- cbind(taxa, df)
tx$colors <- factor(tx$colors, levels = c("salmon", "darkgreen", "cyan", "red", "blue", "plum"))
tax_table(ps.inall.col) <- tax_table(as.matrix(tx))
ord <- ordinate(ps.inall.col, "NMDS", "unifrac")
## Run 0 stress 0.0685455 
## Run 1 stress 0.05568715 
## ... New best solution
## ... Procrustes: rmse 0.04076806  max resid 0.2160826 
## Run 2 stress 0.06784429 
## Run 3 stress 0.05628488 
## Run 4 stress 0.05568719 
## ... Procrustes: rmse 0.0001769095  max resid 0.0006062451 
## ... Similar to previous best
## Run 5 stress 0.07937976 
## Run 6 stress 0.07544596 
## Run 7 stress 0.05628489 
## Run 8 stress 0.05568719 
## ... Procrustes: rmse 0.00002559041  max resid 0.00008856774 
## ... Similar to previous best
## Run 9 stress 0.05568712 
## ... New best solution
## ... Procrustes: rmse 0.00002106782  max resid 0.00006934972 
## ... Similar to previous best
## Run 10 stress 0.06740137 
## Run 11 stress 0.06740136 
## Run 12 stress 0.06784421 
## Run 13 stress 0.06784436 
## Run 14 stress 0.06854546 
## Run 15 stress 0.07953205 
## Run 16 stress 0.05568719 
## ... Procrustes: rmse 0.00004255519  max resid 0.0001401031 
## ... Similar to previous best
## Run 17 stress 0.06740138 
## Run 18 stress 0.06728216 
## Run 19 stress 0.05568718 
## ... Procrustes: rmse 0.0000373923  max resid 0.0001312747 
## ... Similar to previous best
## Run 20 stress 0.07888487 
## *** Solution reached
plot_ordination(ps.inall.col, ord, type = "species", color = "colors") + 
  scale_color_manual(values =  c("salmon", "darkgreen", "cyan", "red", "blue", "plum")) +
  theme_bw() +
  theme(legend.position = "none")

Bray - колбаска равномерна
Поздние стадии слева - при этом ранние кластеры накладываются, поздние разделены Что влияет на ось2? Явно есть какой-то паттерн.

ord <- ordinate(ps.inall.col, "NMDS", "bray")
## Square root transformation
## Wisconsin double standardization
## Run 0 stress 0.09036937 
## Run 1 stress 0.0903694 
## ... Procrustes: rmse 0.00001927814  max resid 0.00007086537 
## ... Similar to previous best
## Run 2 stress 0.09024752 
## ... New best solution
## ... Procrustes: rmse 0.003386048  max resid 0.01505777 
## Run 3 stress 0.09036938 
## ... Procrustes: rmse 0.003390695  max resid 0.01505826 
## Run 4 stress 0.09036937 
## ... Procrustes: rmse 0.003386035  max resid 0.01507802 
## Run 5 stress 0.09036937 
## ... Procrustes: rmse 0.003386432  max resid 0.01505862 
## Run 6 stress 0.1257473 
## Run 7 stress 0.09036937 
## ... Procrustes: rmse 0.003385691  max resid 0.01507976 
## Run 8 stress 0.1268919 
## Run 9 stress 0.09036944 
## ... Procrustes: rmse 0.003410952  max resid 0.01523599 
## Run 10 stress 0.09024752 
## ... New best solution
## ... Procrustes: rmse 0.00003844186  max resid 0.0001638862 
## ... Similar to previous best
## Run 11 stress 0.09036937 
## ... Procrustes: rmse 0.003380784  max resid 0.0150593 
## Run 12 stress 0.09036938 
## ... Procrustes: rmse 0.003379871  max resid 0.01508219 
## Run 13 stress 0.09036939 
## ... Procrustes: rmse 0.003385498  max resid 0.01512324 
## Run 14 stress 0.1358024 
## Run 15 stress 0.09024754 
## ... Procrustes: rmse 0.00003794727  max resid 0.0001665169 
## ... Similar to previous best
## Run 16 stress 0.1258672 
## Run 17 stress 0.1358024 
## Run 18 stress 0.09036937 
## ... Procrustes: rmse 0.003376715  max resid 0.01503468 
## Run 19 stress 0.126985 
## Run 20 stress 0.1360016 
## *** Solution reached
plot_ordination(ps.inall.col, ord, type = "species", color = "colors") + 
  scale_color_manual(values =  c("salmon", "darkgreen", "cyan", "red", "blue", "plum")) +
  theme_bw() +
  theme(legend.position = "none")

0.6.2.3 visualisation

Далее идут одинаковые картинки по всем группам.

l_vst <- color_filt(ps.inall, submod_df)
l_vst

$blue \(blue\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 86 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 3 sample variables ] tax_table() Taxonomy Table: [ 86 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 86 tips and 85 internal nodes ] refseq() DNAStringSet: [ 86 reference sequences ]

\(blue\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 86 89493 0 11387 1819 Avg#Reads 2556.94

Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 86(100%) 86(100%) 86(100%) 85(98.84%) 79(91.86%) 50(58.14%) 7(8.14%)

Metadata variables: 4 SampleID, Day, Description, Group

\(blue\)heat \(blue\)heat_rel \(blue\)tree \(blue\)taxa

Kingdom Phylum Class Order Family Genus Species
Seq314 Bacteria Cyanobacteria Vampirivibrionia Obscuribacterales Obscuribacteraceae NA NA
Seq23 Bacteria Cyanobacteria Vampirivibrionia Obscuribacterales Obscuribacteraceae NA NA
Seq65 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas NA
Seq188 Bacteria Proteobacteria Alphaproteobacteria Reyranellales Reyranellaceae Reyranella soli
Seq334 Bacteria Proteobacteria Alphaproteobacteria Reyranellales Reyranellaceae Reyranella NA
Seq75 Bacteria Proteobacteria Alphaproteobacteria Reyranellales Reyranellaceae Reyranella NA
Seq167 Bacteria Proteobacteria Alphaproteobacteria Reyranellales Reyranellaceae Reyranella massiliensis
Seq273 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Kaistiaceae Kaistia NA
Seq131 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Pseudolabrys NA
Seq138 Bacteria Proteobacteria Alphaproteobacteria Micropepsales Micropepsaceae NA NA
Seq104 Bacteria Proteobacteria Alphaproteobacteria Micropepsales Micropepsaceae NA NA
Seq129 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Altererythrobacter NA
Seq28 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Devosiaceae Devosia NA
Seq360 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Mesorhizobium NA
Seq292 Bacteria Proteobacteria Alphaproteobacteria Caulobacterales Caulobacteraceae NA NA
Seq166 Bacteria Proteobacteria Alphaproteobacteria Caulobacterales Hyphomonadaceae Hirschia NA
Seq39 Bacteria Gemmatimonadota Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae NA NA
Seq30 Bacteria Actinobacteriota Thermoleophilia Solirubrobacterales Solirubrobacteraceae Conexibacter NA
Seq151 Bacteria Actinobacteriota Thermoleophilia Solirubrobacterales 67-14 NA NA
Seq250 Bacteria Actinobacteriota Thermoleophilia Solirubrobacterales 67-14 NA NA
Seq135 Bacteria Myxococcota Polyangia Polyangiales BIrii41 NA NA
Seq46 Bacteria Myxococcota Polyangia Polyangiales BIrii41 NA NA
Seq35 Bacteria Myxococcota Polyangia Polyangiales BIrii41 NA NA
Seq106 Bacteria Myxococcota Polyangia Polyangiales Sandaracinaceae NA NA
Seq345 Bacteria Bdellovibrionota Oligoflexia 0319-6G20 NA NA NA
Seq198 Bacteria Bdellovibrionota Bdellovibrionia Bdellovibrionales Bdellovibrionaceae Bdellovibrio NA
Seq97 Bacteria Bdellovibrionota Bdellovibrionia Bdellovibrionales Bdellovibrionaceae Bdellovibrio NA
Seq183 Bacteria Dependentiae Babeliae Babeliales UBA12409 NA NA
Seq424 Bacteria Actinobacteriota Actinobacteria Propionibacteriales Nocardioidaceae Kribbella NA
Seq136 Bacteria Actinobacteriota Acidimicrobiia Microtrichales Iamiaceae Iamia NA
Seq174 Bacteria Actinobacteriota Acidimicrobiia Microtrichales Iamiaceae Iamia NA
Seq43 Bacteria Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Galbitalea NA
Seq420 Bacteria Actinobacteriota Actinobacteria Micromonosporales Micromonosporaceae Luedemannella NA
Seq127 Bacteria Actinobacteriota Actinobacteria Micromonosporales Micromonosporaceae Dactylosporangium NA
Seq288 Bacteria Actinobacteriota Actinobacteria Streptomycetales Streptomycetaceae NA NA
Seq449 Bacteria Actinobacteriota Actinobacteria Propionibacteriales Propionibacteriaceae Jiangella NA
Seq91 Bacteria Bacteroidota Bacteroidia Bacteroidales NA NA NA
Seq149 Bacteria Bacteroidota Bacteroidia Bacteroidetes VC2.1 Bac22 NA NA NA
Seq169 Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Mucilaginibacter calamicampi
Seq81 Bacteria Bacteroidota Bacteroidia Sphingobacteriales NS11-12 marine group NA NA
Seq211 Bacteria Bacteroidota Bacteroidia NA NA NA NA
Seq119 Bacteria Bacteroidota Bacteroidia Sphingobacteriales env.OPS 17 NA NA
Seq77 Bacteria Spirochaetota Spirochaetia Spirochaetales Spirochaetaceae Salinispira NA
Seq175 Bacteria Spirochaetota Spirochaetia Spirochaetales Spirochaetaceae Spirochaeta 2 NA
Seq305 Bacteria Chloroflexi Anaerolineae Anaerolineales Anaerolineaceae NA NA
Seq379 Bacteria Chloroflexi Chloroflexia Chloroflexales Roseiflexaceae NA NA
Seq165 Bacteria Chloroflexi Chloroflexia Chloroflexales Roseiflexaceae NA NA
Seq327 Bacteria Chloroflexi Chloroflexia Thermomicrobiales JG30-KF-CM45 NA NA
Seq252 Bacteria Armatimonadota Fimbriimonadia Fimbriimonadales Fimbriimonadaceae NA NA
Seq382 Bacteria Verrucomicrobiota Verrucomicrobiae Pedosphaerales Pedosphaeraceae NA NA
Seq123 Bacteria Verrucomicrobiota Verrucomicrobiae Opitutales Opitutaceae Lacunisphaera limnophila
Seq124 Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Terrimicrobiaceae Terrimicrobium NA
Seq325 Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Chthoniobacteraceae LD29 NA
Seq272 Bacteria Verrucomicrobiota Verrucomicrobiae Verrucomicrobiales Verrucomicrobiaceae Roseimicrobium gellanilyticum
Seq402 Bacteria Verrucomicrobiota Verrucomicrobiae Verrucomicrobiales Rubritaleaceae Luteolibacter NA
Seq322 Bacteria Planctomycetota Planctomycetes Pirellulales Pirellulaceae NA NA
Seq356 Bacteria Planctomycetota Planctomycetes Pirellulales Pirellulaceae NA NA
Seq259 Bacteria Planctomycetota Planctomycetes Pirellulales Pirellulaceae Pir4 lineage NA
Seq279 Bacteria Planctomycetota Planctomycetes Pirellulales Pirellulaceae Pir4 lineage NA
Seq214 Bacteria Planctomycetota Planctomycetes Planctomycetales Rubinisphaeraceae SH-PL14 NA
Seq209 Bacteria Planctomycetota Planctomycetes Planctomycetales Schlesneriaceae Schlesneria NA
Seq229 Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales Vicinamibacteraceae NA NA
Seq275 Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales Vicinamibacteraceae NA NA
Seq247 Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales NA NA NA
Seq316 Bacteria Bacteroidota Kapabacteria Kapabacteriales NA NA NA
Seq371 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq12 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq153 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq326 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq10 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae NA NA
Seq82 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Terrimonas NA
Seq462 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Pseudoflavitalea NA
Seq150 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Flavitalea NA
Seq290 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Edaphobaculum NA
Seq339 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Edaphobaculum NA
Seq120 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Taibaiella NA
Seq233 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales 211ds20 NA NA
Seq133 Bacteria Proteobacteria Gammaproteobacteria Steroidobacterales Steroidobacteraceae Steroidobacter flavus
Seq349 Bacteria Proteobacteria Gammaproteobacteria Steroidobacterales Steroidobacteraceae Steroidobacter NA
Seq315 Bacteria Proteobacteria Gammaproteobacteria Gammaproteobacteria Incertae Sedis Unknown Family Acidibacter NA
Seq57 Bacteria Proteobacteria Gammaproteobacteria Gammaproteobacteria Incertae Sedis Unknown Family Acidibacter NA
Seq96 Bacteria Proteobacteria Gammaproteobacteria R7C24 NA NA NA
Seq170 Bacteria Proteobacteria Gammaproteobacteria Gammaproteobacteria Incertae Sedis Unknown Family Acidibacter NA
Seq94 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Rhodanobacteraceae Dokdonella ginsengisoli
Seq114 Bacteria Proteobacteria Gammaproteobacteria Diplorickettsiales Diplorickettsiaceae NA NA
Seq235 Bacteria Proteobacteria Gammaproteobacteria Legionellales Legionellaceae Legionella NA

$cyan \(cyan\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 30 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 3 sample variables ] tax_table() Taxonomy Table: [ 30 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 30 tips and 29 internal nodes ] refseq() DNAStringSet: [ 30 reference sequences ]

\(cyan\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 30 176073 336 15108 4911 Avg#Reads 5030.66

Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 30(100%) 30(100%) 30(100%) 30(100%) 30(100%) 29(96.67%) 2(6.67%)

Metadata variables: 4 SampleID, Day, Description, Group

\(cyan\)heat \(cyan\)heat_rel \(cyan\)tree \(cyan\)taxa

Kingdom Phylum Class Order Family Genus Species
Seq98 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Burkholderiaceae Burkholderia telluris
Seq64 Bacteria Proteobacteria Alphaproteobacteria Azospirillales Inquilinaceae Inquilinus ginsengisoli
Seq4 Bacteria Proteobacteria Alphaproteobacteria Azospirillales Inquilinaceae Inquilinus NA
Seq244 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Pseudorhodoplanes NA
Seq11 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium NA
Seq74 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium NA
Seq22 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Starkeya NA
Seq45 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Allorhizobium NA
Seq9 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Allorhizobium NA
Seq29 Bacteria Myxococcota Polyangia Nannocystales Nannocystaceae Nannocystis NA
Seq239 Bacteria Myxococcota Polyangia Polyangiales Polyangiaceae Labilithrix NA
Seq50 Bacteria Actinobacteriota Actinobacteria Corynebacteriales Mycobacteriaceae Mycobacterium NA
Seq34 Bacteria Actinobacteriota Actinobacteria Streptosporangiales Streptosporangiaceae Herbidospora NA
Seq56 Bacteria Firmicutes Bacilli Paenibacillales Paenibacillaceae Paenibacillus NA
Seq25 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Terribacillus NA
Seq3 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus NA
Seq5 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus NA
Seq13 Bacteria Firmicutes Bacilli Bacillales Planococcaceae NA NA
Seq7 Bacteria Firmicutes Bacilli Bacillales Planococcaceae Solibacillus NA
Seq19 Bacteria Firmicutes Bacilli Bacillales Planococcaceae Solibacillus NA
Seq17 Bacteria Planctomycetota Planctomycetes Isosphaerales Isosphaeraceae Singulisphaera NA
Seq324 Bacteria Acidobacteriota Acidobacteriae Acidobacteriales Acidobacteriaceae (Subgroup 1) Edaphobacter NA
Seq16 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq6 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq1 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq109 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq49 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Taibaiella NA
Seq73 Bacteria Bacteroidota Bacteroidia Cytophagales Spirosomaceae Dyadobacter NA
Seq15 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Rhodanobacteraceae Luteibacter NA
Seq26 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Luteimonas NA

$darkgreen \(darkgreen\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 44 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 3 sample variables ] tax_table() Taxonomy Table: [ 44 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 44 tips and 43 internal nodes ] refseq() DNAStringSet: [ 44 reference sequences ]

\(darkgreen\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 44 12360 0 2468 65 Avg#Reads 353.14

Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 44(100%) 44(100%) 44(100%) 43(97.73%) 40(90.91%) 24(54.55%) 3(6.82%)

Metadata variables: 4 SampleID, Day, Description, Group

\(darkgreen\)heat \(darkgreen\)heat_rel \(darkgreen\)tree \(darkgreen\)taxa

Kingdom Phylum Class Order Family Genus Species
Seq342 Archaea Crenarchaeota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae NA NA
Seq196 Archaea Crenarchaeota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae Candidatus Nitrocosmicus NA
Seq276 Archaea Crenarchaeota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae NA NA
Seq419 Archaea Crenarchaeota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae NA NA
Seq454 Bacteria Proteobacteria Gammaproteobacteria Diplorickettsiales Diplorickettsiaceae Aquicella NA
Seq329 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas jaspsi
Seq332 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Magnetospiraceae NA NA
Seq429 Bacteria Proteobacteria Alphaproteobacteria Acetobacterales Acetobacteraceae NA NA
Seq195 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Pseudorhodoplanes NA
Seq144 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Pseudolabrys NA
Seq369 Bacteria Proteobacteria Alphaproteobacteria Micropepsales Micropepsaceae NA NA
Seq362 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Altererythrobacter NA
Seq428 Bacteria Proteobacteria Alphaproteobacteria Caulobacterales Caulobacteraceae Phenylobacterium NA
Seq347 Bacteria Nitrospirota Nitrospiria Nitrospirales Nitrospiraceae Nitrospira japonica
Seq328 Bacteria Myxococcota Polyangia Haliangiales Haliangiaceae Haliangium NA
Seq348 Bacteria Myxococcota Polyangia Polyangiales BIrii41 NA NA
Seq308 Bacteria Myxococcota Polyangia Polyangiales BIrii41 NA NA
Seq256 Bacteria Myxococcota Polyangia Polyangiales Polyangiaceae Minicystis NA
Seq302 Bacteria Bdellovibrionota Oligoflexia 0319-6G20 NA NA NA
Seq435 Bacteria Actinobacteriota Actinobacteria Propionibacteriales Propionibacteriaceae Microlunatus NA
Seq291 Bacteria Actinobacteriota Acidimicrobiia IMCC26256 NA NA NA
Seq392 Bacteria Actinobacteriota Acidimicrobiia Microtrichales Ilumatobacteraceae NA NA
Seq321 Bacteria Bacteroidota Bacteroidia Sphingobacteriales NS11-12 marine group NA NA
Seq186 Bacteria Firmicutes Bacilli Paenibacillales Paenibacillaceae Paenibacillus NA
Seq204 Bacteria Firmicutes Bacilli Bacillales Planococcaceae Paenisporosarcina NA
Seq146 Bacteria Spirochaetota Spirochaetia Spirochaetales Spirochaetaceae Spirochaeta 2 NA
Seq359 Bacteria Patescibacteria Saccharimonadia Saccharimonadales LWQ8 NA NA
Seq269 Bacteria Chloroflexi Chloroflexia Chloroflexales Roseiflexaceae NA NA
Seq267 Bacteria Verrucomicrobiota Verrucomicrobiae Opitutales Opitutaceae Lacunisphaera NA
Seq320 Bacteria Verrucomicrobiota Verrucomicrobiae Opitutales Opitutaceae Opitutus NA
Seq203 Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Terrimicrobiaceae Terrimicrobium NA
Seq497 Bacteria Planctomycetota Planctomycetes Pirellulales Pirellulaceae NA NA
Seq384 Bacteria Planctomycetota Planctomycetes Planctomycetales NA NA NA
Seq155 Bacteria Acidobacteriota Blastocatellia Blastocatellales Blastocatellaceae NA NA
Seq350 Bacteria Bacteroidota Bacteroidia Sphingobacteriales env.OPS 17 NA NA
Seq224 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Terrimonas NA
Seq409 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Edaphobaculum NA
Seq337 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Taibaiella NA
Seq494 Bacteria Bacteroidota Bacteroidia Cytophagales Amoebophilaceae Candidatus Amoebophilus NA
Seq277 Bacteria Proteobacteria Gammaproteobacteria NA NA NA NA
Seq191 Bacteria Proteobacteria Gammaproteobacteria Gammaproteobacteria Incertae Sedis Unknown Family Acidibacter NA
Seq335 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Luteimonas vadosa
Seq157 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Rhodanobacteraceae Dokdonella NA
Seq385 Bacteria Proteobacteria Gammaproteobacteria Salinisphaerales Solimonadaceae NA NA

$plum \(plum\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 30 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 3 sample variables ] tax_table() Taxonomy Table: [ 30 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 30 tips and 29 internal nodes ] refseq() DNAStringSet: [ 30 reference sequences ]

\(plum\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 30 17172 0 3034 103 Avg#Reads 490.63

Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 30(100%) 30(100%) 30(100%) 30(100%) 27(90%) 16(53.33%) 1(3.33%)

Metadata variables: 4 SampleID, Day, Description, Group

\(plum\)heat \(plum\)heat_rel \(plum\)tree \(plum\)taxa

Kingdom Phylum Class Order Family Genus Species
Seq161 Bacteria Proteobacteria Gammaproteobacteria Diplorickettsiales Diplorickettsiaceae Aquicella NA
Seq181 Bacteria Proteobacteria Gammaproteobacteria CCD24 NA NA NA
Seq207 Bacteria Cyanobacteria Vampirivibrionia Obscuribacterales Obscuribacteraceae NA NA
Seq219 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas naasensis
Seq216 Bacteria Proteobacteria Alphaproteobacteria Dongiales Dongiaceae Dongia NA
Seq220 Bacteria Proteobacteria Alphaproteobacteria Reyranellales Reyranellaceae Reyranella NA
Seq90 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Pseudolabrys NA
Seq271 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae NA NA
Seq111 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingobium NA
Seq33 Bacteria Proteobacteria Alphaproteobacteria Caulobacterales Caulobacteraceae Caulobacter NA
Seq189 Bacteria Actinobacteriota Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter NA
Seq85 Bacteria Myxococcota Polyangia Polyangiales BIrii41 NA NA
Seq208 Bacteria Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Galbitalea NA
Seq218 Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Mucilaginibacter NA
Seq215 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus NA
Seq177 Bacteria Fibrobacterota Fibrobacteria Fibrobacterales Fibrobacteraceae NA NA
Seq375 Bacteria Chloroflexi Chloroflexia Thermomicrobiales JG30-KF-CM45 NA NA
Seq430 Bacteria Planctomycetota Phycisphaerae Phycisphaerales Phycisphaeraceae NA NA
Seq368 Bacteria Planctomycetota Planctomycetes Pirellulales Pirellulaceae NA NA
Seq152 Bacteria Planctomycetota Planctomycetes Gemmatales Gemmataceae Gemmata NA
Seq304 Bacteria Planctomycetota Planctomycetes Planctomycetales NA NA NA
Seq141 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Terrimonas NA
Seq343 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae NA NA
Seq412 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Edaphobaculum NA
Seq457 Bacteria Proteobacteria Gammaproteobacteria Coxiellales Coxiellaceae Coxiella NA
Seq130 Bacteria Proteobacteria Gammaproteobacteria R7C24 NA NA NA
Seq346 Bacteria Proteobacteria Gammaproteobacteria Salinisphaerales Solimonadaceae Alkanibacter NA
Seq474 Bacteria Proteobacteria Gammaproteobacteria Diplorickettsiales Diplorickettsiaceae NA NA
Seq472 Bacteria Proteobacteria Gammaproteobacteria Diplorickettsiales Diplorickettsiaceae NA NA
Seq227 Bacteria Proteobacteria Gammaproteobacteria Diplorickettsiales Diplorickettsiaceae NA NA

$red \(red\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 75 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 3 sample variables ] tax_table() Taxonomy Table: [ 75 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 75 tips and 74 internal nodes ] refseq() DNAStringSet: [ 75 reference sequences ]

\(red\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 75 66650 241 5339 1528 Avg#Reads 1904.29

Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 75(100%) 75(100%) 75(100%) 74(98.67%) 74(98.67%) 66(88%) 11(14.67%)

Metadata variables: 4 SampleID, Day, Description, Group

\(red\)heat \(red\)heat_rel \(red\)tree \(red\)taxa

Kingdom Phylum Class Order Family Genus Species
Seq117 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Burkholderiaceae Burkholderia NA
Seq60 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Alcaligenaceae NA NA
Seq121 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Comamonadaceae Variovorax NA
Seq383 Bacteria Proteobacteria Alphaproteobacteria Ferrovibrionales Ferrovibrionaceae Ferrovibrio soli
Seq228 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae NA NA
Seq178 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Methylobacterium-Methylorubrum NA
Seq171 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Bosea thiooxidans
Seq341 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Bosea NA
Seq89 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Tardiphaga robiniae
Seq31 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Starkeya NA
Seq160 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Hyphomicrobiaceae Hyphomicrobium NA
Seq251 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingopyxis NA
Seq373 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Altererythrobacter NA
Seq108 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Mesorhizobium NA
Seq71 Bacteria Actinobacteriota Thermoleophilia Solirubrobacterales Solirubrobacteraceae Conexibacter NA
Seq338 Bacteria Myxococcota Polyangia Polyangiales Polyangiaceae Pajaroellobacter NA
Seq230 Bacteria Myxococcota Polyangia Polyangiales Polyangiaceae Pajaroellobacter NA
Seq88 Bacteria Myxococcota Polyangia Polyangiales Polyangiaceae Sorangium NA
Seq303 Bacteria Actinobacteriota Acidimicrobiia Microtrichales Ilumatobacteraceae NA NA
Seq93 Bacteria Actinobacteriota Actinobacteria Micrococcales Promicromonosporaceae Promicromonospora NA
Seq366 Bacteria Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Leifsonia NA
Seq134 Bacteria Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae NA aoyamense
Seq411 Bacteria Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Agromyces NA
Seq115 Bacteria Actinobacteriota Actinobacteria Corynebacteriales Mycobacteriaceae Mycobacterium NA
Seq128 Bacteria Actinobacteriota Actinobacteria Streptosporangiales Streptosporangiaceae Herbidospora mongoliensis
Seq398 Bacteria Actinobacteriota Actinobacteria Streptosporangiales Streptosporangiaceae Nonomuraea NA
Seq78 Bacteria Actinobacteriota Actinobacteria Streptosporangiales Thermomonosporaceae Actinocorallia NA
Seq193 Bacteria Actinobacteriota Actinobacteria Streptomycetales Streptomycetaceae Streptomyces NA
Seq148 Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Pedobacter NA
Seq307 Bacteria Bacteroidota Bacteroidia Sphingobacteriales NS11-12 marine group NA NA
Seq431 Bacteria Bacteroidota Bacteroidia Sphingobacteriales NS11-12 marine group NA NA
Seq205 Bacteria Firmicutes Bacilli Paenibacillales Paenibacillaceae Paenibacillus lautus
Seq86 Bacteria Firmicutes Bacilli Paenibacillales Paenibacillaceae Paenibacillus NA
Seq51 Bacteria Firmicutes Bacilli Paenibacillales Paenibacillaceae Paenibacillus NA
Seq18 Bacteria Firmicutes Bacilli Paenibacillales Paenibacillaceae Paenibacillus NA
Seq192 Bacteria Firmicutes Bacilli Paenibacillales Paenibacillaceae Paenibacillus NA
Seq266 Bacteria Firmicutes Bacilli Paenibacillales Paenibacillaceae Paenibacillus NA
Seq278 Bacteria Firmicutes Bacilli Bacillales Planococcaceae Domibacillus NA
Seq99 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus NA
Seq53 Bacteria Firmicutes Bacilli Bacillales Planococcaceae Lysinibacillus NA
Seq118 Bacteria Firmicutes Bacilli Bacillales Planococcaceae Lysinibacillus NA
Seq76 Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Terrimicrobiaceae Terrimicrobium NA
Seq232 Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Terrimicrobiaceae Terrimicrobium NA
Seq168 Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Terrimicrobiaceae Terrimicrobium NA
Seq387 Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Chthoniobacteraceae Chthoniobacter NA
Seq285 Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Chthoniobacteraceae Chthoniobacter NA
Seq217 Bacteria Verrucomicrobiota Verrucomicrobiae Verrucomicrobiales Verrucomicrobiaceae Verrucomicrobium spinosum
Seq190 Bacteria Planctomycetota Planctomycetes Gemmatales Gemmataceae Gemmata NA
Seq249 Bacteria Planctomycetota Planctomycetes Isosphaerales Isosphaeraceae Singulisphaera NA
Seq254 Bacteria Acidobacteriota Acidobacteriae Acidobacteriales Acidobacteriaceae (Subgroup 1) Edaphobacter NA
Seq67 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq176 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq268 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Pseudoflavitalea NA
Seq32 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Pseudoflavitalea NA
Seq84 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Pseudoflavitalea NA
Seq459 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Niastella NA
Seq40 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Niastella hibisci
Seq173 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Niastella NA
Seq246 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Niastella NA
Seq112 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Flavitalea NA
Seq126 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga ginsengihumi
Seq102 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga arvensicola
Seq309 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga soli
Seq70 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq262 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq301 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Taibaiella NA
Seq572 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae NA NA
Seq436 Bacteria Proteobacteria Gammaproteobacteria Steroidobacterales Steroidobacteraceae Steroidobacter NA
Seq261 Bacteria Proteobacteria Gammaproteobacteria Gammaproteobacteria Incertae Sedis Unknown Family Acidibacter NA
Seq298 Bacteria Proteobacteria Gammaproteobacteria Gammaproteobacteria Incertae Sedis Unknown Family Acidibacter NA
Seq354 Bacteria Proteobacteria Gammaproteobacteria Gammaproteobacteria Incertae Sedis Unknown Family Acidibacter NA
Seq226 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Rhodanobacteraceae Tahibacter NA
Seq147 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Xanthomonas NA
Seq370 Bacteria Proteobacteria Gammaproteobacteria Diplorickettsiales Diplorickettsiaceae NA NA
Seq486 Bacteria Proteobacteria Gammaproteobacteria NA NA NA NA

$salmon \(salmon\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 73 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 3 sample variables ] tax_table() Taxonomy Table: [ 73 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 73 tips and 72 internal nodes ] refseq() DNAStringSet: [ 73 reference sequences ]

\(salmon\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 73 115332 0 20534 779 Avg#Reads 3295.2

Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 73(100%) 73(100%) 73(100%) 72(98.63%) 71(97.26%) 66(90.41%) 12(16.44%)

Metadata variables: 4 SampleID, Day, Description, Group

\(salmon\)heat \(salmon\)heat_rel \(salmon\)tree \(salmon\)taxa

Kingdom Phylum Class Order Family Genus Species
Seq79 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Oxalobacteraceae Massilia armeniaca
Seq122 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Oxalobacteraceae NA NA
Seq179 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Oxalobacteraceae Pseudoduganella NA
Seq145 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Oxalobacteraceae Pseudoduganella eburnea
Seq154 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Oxalobacteraceae Massilia NA
Seq222 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Oxalobacteraceae Massilia NA
Seq159 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Burkholderiaceae Cupriavidus NA
Seq8 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Burkholderiaceae Cupriavidus NA
Seq14 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Alcaligenaceae Achromobacter NA
Seq54 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Comamonadaceae NA paradoxus
Seq95 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Comamonadaceae Xylophilus NA
Seq340 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Comamonadaceae Rhizobacter NA
Seq264 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas mucosissima
Seq333 Bacteria Proteobacteria Alphaproteobacteria Reyranellales Reyranellaceae Reyranella NA
Seq158 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga NA
Seq248 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Allorhizobium NA
Seq245 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Devosiaceae Devosia neptuniae
Seq185 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Shinella NA
Seq156 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae NA NA
Seq42 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae NA NA
Seq286 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Ensifer NA
Seq21 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Allorhizobium NA
Seq107 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Neorhizobium NA
Seq231 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Allorhizobium azooxidifex
Seq140 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae NA NA
Seq378 Bacteria Proteobacteria Alphaproteobacteria Caulobacterales Caulobacteraceae Phenylobacterium mobile
Seq374 Bacteria Myxococcota Polyangia Haliangiales Haliangiaceae Haliangium NA
Seq257 Bacteria Myxococcota Polyangia Polyangiales Polyangiaceae Pajaroellobacter NA
Seq223 Bacteria Actinobacteriota Actinobacteria Micrococcales Promicromonosporaceae Cellulosimicrobium NA
Seq83 Bacteria Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Microbacterium NA
Seq68 Bacteria Actinobacteriota Actinobacteria Corynebacteriales Mycobacteriaceae Mycobacterium NA
Seq293 Bacteria Actinobacteriota Actinobacteria Glycomycetales Glycomycetaceae Glycomyces NA
Seq72 Bacteria Actinobacteriota Actinobacteria Streptomycetales Streptomycetaceae Streptomyces NA
Seq101 Bacteria Actinobacteriota Actinobacteria Streptomycetales Streptomycetaceae Streptomyces NA
Seq265 Bacteria Actinobacteriota Actinobacteria Streptomycetales Streptomycetaceae Streptomyces NA
Seq260 Bacteria Bacteroidota Bacteroidia Sphingobacteriales NA NA NA
Seq180 Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Pedobacter panaciterrae
Seq142 Bacteria Verrucomicrobiota Verrucomicrobiae Verrucomicrobiales Verrucomicrobiaceae Roseimicrobium NA
Seq163 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq253 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq116 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq184 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq52 Bacteria Bacteroidota Bacteroidia Flavobacteriales Flavobacteriaceae Flavobacterium NA
Seq187 Bacteria Bacteroidota Bacteroidia Flavobacteriales Weeksellaceae Chryseobacterium ginsenosidimutans
Seq172 Bacteria Bacteroidota Bacteroidia Flavobacteriales Weeksellaceae Chryseobacterium NA
Seq283 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Flavitalea NA
Seq113 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Niastella NA
Seq110 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Niastella NA
Seq132 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Pseudoflavitalea NA
Seq37 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq162 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq182 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga humicola
Seq92 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq80 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga pinensis
Seq2 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq221 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq20 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq282 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq38 Bacteria Bacteroidota Bacteroidia Cytophagales Spirosomaceae Dyadobacter NA
Seq237 Bacteria Proteobacteria Gammaproteobacteria Steroidobacterales Steroidobacteraceae Steroidobacter agariperforans
Seq234 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Pseudoxanthomonas NA
Seq59 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Stenotrophomonas NA
Seq105 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Stenotrophomonas NA
Seq344 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Lysobacter NA
Seq41 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Lysobacter NA
Seq243 Bacteria Proteobacteria Gammaproteobacteria NA NA NA NA
Seq406 Bacteria Proteobacteria Gammaproteobacteria Legionellales Legionellaceae Legionella NA
Seq139 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas NA
Seq24 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas NA
Seq27 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas NA
Seq87 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas NA
Seq55 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas NA
Seq201 Bacteria Proteobacteria Gammaproteobacteria Enterobacterales Enterobacteriaceae Klebsiella NA

mpd по стадиям

physeq_merged <- merge_samples(ps.f, "Group", fun=sum)
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
## Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
## Also defined by 'tidytree'
ps.f@sam_data
##                 Day Description  Group
## straw-16s-D01-1 D01       D01_1  early
## straw-16s-D01-2 D01       D01_2  early
## straw-16s-D01-3 D01       D01_3  early
## straw-16s-D03-1 D03       D03_1  early
## straw-16s-D03-2 D03       D03_2  early
## straw-16s-D03-3 D03       D03_3  early
## straw-16s-D05-1 D05       D05_1  early
## straw-16s-D05-2 D05       D05_2  early
## straw-16s-D05-3 D05       D05_3  early
## straw-16s-D05-4 D05       D05_4  early
## straw-16s-D05-5 D05       D05_5  early
## straw-16s-D07-2 D07       D07_2 middle
## straw-16s-D07-3 D07       D07_3 middle
## straw-16s-D08-1 D08       D08_1 middle
## straw-16s-D08-2 D08       D08_2 middle
## straw-16s-D08-3 D08       D08_3 middle
## straw-16s-D10-1 D10       D10_1 middle
## straw-16s-D10-2 D10       D10_2 middle
## straw-16s-D10-3 D10       D10_3 middle
## straw-16s-D10-4 D10       D10_4 middle
## straw-16s-D10-5 D10       D10_5 middle
## straw-16s-D12-1 D12       D12_1   late
## straw-16s-D12-2 D12       D12_2   late
## straw-16s-D12-3 D12       D12_3   late
## straw-16s-D13-1 D13       D13_1   late
## straw-16s-D13-2 D13       D13_2   late
## straw-16s-D13-3 D13       D13_3   late
## straw-16s-D14-1 D14       D14_1   late
## straw-16s-D14-2 D14       D14_2   late
## straw-16s-D14-3 D14       D14_3   late
## straw-16s-D14-4 D14       D14_4   late
## straw-16s-D14-5 D14       D14_5   late
## straw-16s-D15-1 D15       D15_1   late
## straw-16s-D15-2 D15       D15_2   late
## straw-16s-D15-3 D15       D15_3   late
# picante::mpd(l_vst$blue$ps@otu_table@.Data, cophenetic(l_vst$blue$ps@phy_tree)) %>% 
#   mean(na.rm = TRUE)
# 
# picante::mpd(l_vst$salmon$ps@otu_table@.Data, cophenetic(l_vst$salmon$ps@phy_tree)) %>% 
#   mean(na.rm = TRUE)

picante::ses.mpd(physeq_merged@otu_table@.Data, cophenetic(physeq_merged@phy_tree)) 
##        ntaxa  mpd.obs mpd.rand.mean mpd.rand.sd mpd.obs.rank  mpd.obs.z
## early    364 1.742096      1.862383  0.02930118            1 -4.1051776
## middle   490 1.839665      1.863938  0.02298162          147 -1.0561720
## late     822 1.877129      1.863599  0.01354403          842  0.9989395
##        mpd.obs.p runs
## early      0.001  999
## middle     0.147  999
## late       0.842  999

0.7 Add a metadata

list.files("meta/")
## [1] "cell_realtime_stat.xlsx" "cell_resp_ch_stat.xlsx" 
## [3] "period_legend.xlsx"

period_legend - соответствие номеров мешочков в 16S с днями, думаю лучше заменить везде обозначения 1, 3 и тд на дни cell_resp - данные по дыханию, по ним какую-нибудь простую статистику. Да, повторностей для эксперимента и контроля разное количество cell_realtime - это циклы выхода целлюлаз по реалтайму, я их нормировала по 16S, есть в этой же таблице. Что с ними делать особо не знаю, вроде вообще решили выкинуть

realtime.data <- readxl::read_excel("meta/cell_realtime_stat.xlsx")
period.data <- readxl::read_excel("meta/period_legend.xlsx")
resp.data <- readxl::read_excel("meta/cell_resp_ch_stat.xlsx")
realtime.data
## # A tibble: 36 × 29
##    id        day contr…¹ CELL_…² CELL_…³ CELL_…⁴ CELL_…⁵ CELL_…⁶ CELL_…⁷ CELL_…⁸
##    <chr>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>
##  1 G01-1-1     3    15.6    33.2    31.1    33.6    36.6    33.8    38.0    33.0
##  2 G01-1-2     3    15.5    33.3    31.3    32.9    36.2    33.8    41      32.7
##  3 G01-1-3     3    15.5    33.6    31.2    32.9    35.8    33.3    38.2    32.9
##  4 G01-2-1     3    17.1    36.0    31.1    33.1    36.9    36.4    38.8    33.8
##  5 G01-2-2     3    17.3    35.6    31.0    32.8    37.8    35.7    40.1    33.6
##  6 G01-2-3     3    17.1    36      31.1    32.8    38.1    35.2    37.6    33.6
##  7 G01-3-1     3    16.4    35.4    31.6    34.9    39.1    35.3    40.9    33.2
##  8 G01-3-2     3    16.5    35.6    31.3    34.4    37.9    34.6    38.9    33.1
##  9 G01-3-3     3    16.4    35.8    31.5    34.4    41.6    35.0    36.5    33.4
## 10 G05-1-1    28    18.2    26.3    29.1    29.4    28.2    28.4    37.4    34.5
## # … with 26 more rows, 19 more variables: CELL_193122 <dbl>, CELL_73229 <dbl>,
## #   CELL_47814 <dbl>, CELL_163125 <dbl>, CELL_73266 <dbl>, CELL_88582 <dbl>,
## #   CELL_63583 <dbl>, CELL_14199 <dbl>, CELL_95616 <dbl>, CELL_63504 <dbl>,
## #   CELL_08643 <chr>, CELL_199599 <dbl>, CELL_01426 <dbl>, CELL_71601 <dbl>,
## #   CELL_45099 <dbl>, CELL_191900 <dbl>, CELL_99463 <dbl>, CELL_74579 <dbl>,
## #   CELL_183403 <dbl>, and abbreviated variable names ¹​contr_16S, ²​CELL_172283,
## #   ³​CELL_203163, ⁴​CELL_83325, ⁵​CELL_188413, ⁶​CELL_109631, ⁷​CELL_188119, …

0.7.1 Realtime data

impute.mean <- function(x) replace(x, is.na(x), mean(x, na.rm = TRUE))

realtime_data <- realtime.data %>% 
  mutate(CELL_08643 = as.numeric(CELL_08643)) %>% 
  group_by(day) %>%
  mutate(nice_cell = impute.mean(CELL_08643)) %>% 
  mutate(day = as.factor(day))
## Warning in mask$eval_all_mutate(quo): NAs introduced by coercion
realtime_zjena <- readxl::read_excel("cellulases_gene_expression(1).xlsx")
geom_mean <-function(x){exp(mean(log(x)))}

realtime_zjena_geom <- realtime_zjena %>% 
  mutate(repeats = paste0(realtime_zjena$week, "-", rep(1:3, 3, each=3))) %>% 
  relocate(repeats, 1) %>% 
  group_by(repeats) %>% 
  summarise_if(is.numeric, geom_mean) %>% 
  mutate(week = as.factor(week)) %>% 
  arrange(week)

UPGMA целлюлаз(дистанция - брей).
Не очень понимаю, что это значит. В зависимости от дистанции получаются совсем разные кластеризации.

realtime_matrix <- realtime_zjena_geom %>% 
  column_to_rownames("repeats") %>% 
  select_if(is.numeric) %>% 
  as.matrix()

hcl <- hclust(vegan::vegdist(t(realtime_matrix), method="bray"), "average")
plot(hcl)

А вот - евклидова дистанция.
Ничего общего с предыдущей картинкой

hcl <- hclust(vegan::vegdist(t(realtime_matrix), method="euclidian"), "average")
plot(hcl)

Корплот целлюлаз.
Только корреляции

m = cor(realtime_matrix)
corrplot::corrplot(m)

Только достоверные корреляции
В общем - кластеры есть - но корреляцие недостоверные(за некоторыми исключениями)

cor_test_mat <- psych::corr.test(realtime_matrix)$p
corrplot::corrplot(m, p.mat = cor_test_mat, method = 'circle', type = 'lower', insig='blank',
         order = 'AOE', diag = FALSE)$corrPos -> p1

# text(p1$x, p1$y, round(p1$corr, 2))

То же, но матрица уже прологарифмирована.

cor_test_mat <- psych::corr.test(log(realtime_matrix))
corrplot::corrplot(cor_test_mat$r, p.mat = cor_test_mat$p, method = 'circle', type = 'lower', insig='blank',
         order = 'AOE', diag = FALSE)$corrPos -> p1

# text(p1$x, p1$y, round(p1$corr, 2))

add phylogenic tree (mafft - iqtree(ML))

realtime_tree <- ape::read.tree("al_chz.fasta.contree")
plot(realtime_tree)

library(tidyverse)

realtime_data %>% 
  select(c("day", "id", "contr_16S", "CELL_172283")) %>% 
  mutate(bio_repl = gsub("-[1-3]$", "", id)) %>% 
  group_by(bio_repl, day) %>% 
  summarise(contr_tmean = mean(contr_16S),
            data_tmean = mean(CELL_172283)) %>% 
  mutate(dCt = data_tmean - contr_tmean)
## `summarise()` has grouped output by 'bio_repl'. You can override using the
## `.groups` argument.
## # A tibble: 12 × 5
## # Groups:   bio_repl [12]
##    bio_repl day   contr_tmean data_tmean   dCt
##    <chr>    <fct>       <dbl>      <dbl> <dbl>
##  1 G01-1    3            15.5       33.4 17.8 
##  2 G01-2    3            17.2       35.9 18.7 
##  3 G01-3    3            16.4       35.6 19.2 
##  4 G05-1    28           18.4       26.2  7.81
##  5 G05-2    28           16.5       26.2  9.73
##  6 G05-3    28           18.5       32.0 13.6 
##  7 G10-1    91           17.4       26.2  8.72
##  8 G10-2    91           16.3       24.1  7.79
##  9 G10-3    91           17.5       26.3  8.81
## 10 G14-1    161          18.0       28.1 10.1 
## 11 G14-2    161          16.5       27.0 10.6 
## 12 G14-3    161          16.9       25.4  8.41
resp_data <- resp.data %>% 
  group_by(day) %>%
  mutate(control = impute.mean(control)) %>% 
  mutate(straw = impute.mean(straw)) 

resp_data
## # A tibble: 164 × 3
## # Groups:   day [27]
##      day control straw
##    <dbl>   <dbl> <dbl>
##  1     0    250   250 
##  2     3    285.  723.
##  3     3    263.  832.
##  4     3    131.  657.
##  5     3    307.  525.
##  6     3    241.  744.
##  7     3    245.  701.
##  8     3    245.  657.
##  9     7    274.  690.
## 10     7    296.  690.
## # … with 154 more rows

0.7.2 Knee plot

Дыхание - median(straw)/median(control)

Mожно использовать сторонний пакет(KneeArrower) что понять в каком месте knee_plot происходит перелом. Для элиминации повторностей возьмем медиану.   Я хз как этот пакет работает(ищет производную, но как сглаживает - хз, там матан), но он говорит что перелом происходит скорее на 60-80 днях.

(я исправил ошибки - стало ближе к твоим данным)

https://github.com/agentlans/KneeArrower - вот здесь можно почитать про матан

# resp_data %>% 
#   filter(!day == 0) %>% 
#   group_by(day) %>% 
#   summarise(median_control = median(control),
#             median_straw = median(straw)) %>% 
#   mutate(rel = median_straw/median_control) %>% 
#   ggplot() +
#   geom_point(aes(x = day, y = rel))

resp_median <- resp_data %>% 
  filter(!day == 0) %>% 
  group_by(day) %>% 
  summarise(median_control = median(control),
            median_straw = median(straw)) %>% 
  mutate(rel = median_straw/median_control)


thresholds <- c(0.25, 0.5, 0.75, 1)

# Find cutoff points at each threshold
cutoff.points <- lapply(thresholds, function(i) {
  findCutoff(resp_median$day, resp_median$rel, method="first", i)
})

x.coord <- sapply(cutoff.points, function(p) p$x)
y.coord <- sapply(cutoff.points, function(p) p$y)

# Plot the cutoff points on the scatterplot
plot(resp_median$day, resp_median$rel, pch=20, col="gray")
points(x.coord, y.coord, col="red", pch=20)
text(x.coord, y.coord, labels=thresholds, pos=4, col="red")

period_data <- period.data %>%
  mutate(bag_id = as.factor(bag_id))

period_data
## # A tibble: 15 × 2
##    bag_id   day
##    <fct>  <dbl>
##  1 1          3
##  2 2          7
##  3 3         14
##  4 4         21
##  5 5         28
##  6 6         35
##  7 7         49
##  8 8         63
##  9 9         77
## 10 10        91
## 11 11       105
## 12 12       119
## 13 13       140
## 14 14       161
## 15 15       182

0.7.3 альфа/дыхание

Ну я вот не очень понимаю что делать дальше - привязать кластеры к этой картинке?

resp_median_bags <- resp_median %>% 
  left_join(period.data, by="day") %>% 
  mutate(bag_id = as.factor(bag_id))

ps.f.r <- rarefy_even_depth(ps.f)

estimate_richness(ps.f.r) %>% 
  rownames_to_column("ID") %>% 
  mutate(bag_id = as.factor(
    as.numeric(
      gsub("\\..+","",
           gsub("straw\\.16s\\.D","", ID)
           )
      )
    )
    ) %>% 
  group_by(bag_id) %>% 
  summarise(Observed = mean(Observed),
            Shannon = mean(Shannon),
            InvSimpson = mean(InvSimpson)) %>% 
  left_join(period_data, by="bag_id") %>% 
  left_join(resp_median_bags, by="bag_id") %>% 
  mutate(
    Observed_scaled = scale(Observed),
    Shannon_scaled = scale(Shannon),
    InvSimpson_scaled = scale(InvSimpson),
    Respiration_scaled = scale(rel)
  ) %>% 
  select(c(bag_id, Observed_scaled, Shannon_scaled, InvSimpson_scaled, Respiration_scaled)) %>% 
  pivot_longer(c("Observed_scaled", "Shannon_scaled", "InvSimpson_scaled", "Respiration_scaled")) %>% 
  ggplot(aes(y = value, x = bag_id, group = name)) +
  geom_line(aes(color = name),
            alpha = 0.8) +
  theme_bw()

Корреляция -ртрицательная слабенькая, не особо достоверная и только Пирсона(которая работает для нормального распределения(у нас хроносерия, надо спирмана по хорошему))

alpha_resp <- phyloseq::estimate_richness(ps.f.r) %>% 
  rownames_to_column("ID") %>% 
  mutate(bag_id = as.factor(
    as.numeric(
      gsub("\\..+","",
           gsub("straw\\.16s\\.D","", ID)
           )
      )
    )
    ) %>% 
  group_by(bag_id) %>% 
  summarise(Observed = mean(Observed),
            Shannon = mean(Shannon),
            InvSimpson = mean(InvSimpson)) %>% 
  left_join(period_data, by="bag_id") %>% 
  left_join(resp_median_bags, by="bag_id") %>% 
  mutate(
    Observed_scaled = scale(Observed),
    Shannon_scaled = scale(Shannon),
    InvSimpson_scaled = scale(InvSimpson),
    Respiration_scaled = scale(rel)
  ) %>% 
  select(c(bag_id, Observed_scaled, Shannon_scaled, InvSimpson_scaled, Respiration_scaled))

cor.test(alpha_resp$Observed_scaled, alpha_resp$Respiration_scaled, method = "spearman")
## 
##  Spearman's rank correlation rho
## 
## data:  alpha_resp$Observed_scaled and alpha_resp$Respiration_scaled
## S = 230, p-value = 0.2629
## alternative hypothesis: true rho is not equal to 0
## sample estimates:
##        rho 
## -0.3939394
cor.test(alpha_resp$Shannon_scaled, alpha_resp$Respiration_scaled, method = "spearman")
## 
##  Spearman's rank correlation rho
## 
## data:  alpha_resp$Shannon_scaled and alpha_resp$Respiration_scaled
## S = 232, p-value = 0.2474
## alternative hypothesis: true rho is not equal to 0
## sample estimates:
##        rho 
## -0.4060606
cor.test(alpha_resp$InvSimpson_scaled, alpha_resp$Respiration_scaled, method = "spearman")
## 
##  Spearman's rank correlation rho
## 
## data:  alpha_resp$InvSimpson_scaled and alpha_resp$Respiration_scaled
## S = 226, p-value = 0.2956
## alternative hypothesis: true rho is not equal to 0
## sample estimates:
##       rho 
## -0.369697
cor.test(alpha_resp$Observed_scaled, alpha_resp$Respiration_scaled, method = "pearson")
## 
##  Pearson's product-moment correlation
## 
## data:  alpha_resp$Observed_scaled and alpha_resp$Respiration_scaled
## t = -2.7571, df = 8, p-value = 0.02479
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
##  -0.9223009 -0.1220128
## sample estimates:
##        cor 
## -0.6980158
cor.test(alpha_resp$Shannon_scaled, alpha_resp$Respiration_scaled, method = "pearson")
## 
##  Pearson's product-moment correlation
## 
## data:  alpha_resp$Shannon_scaled and alpha_resp$Respiration_scaled
## t = -2.8453, df = 8, p-value = 0.02164
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
##  -0.9255437 -0.1437787
## sample estimates:
##        cor 
## -0.7092031
cor.test(alpha_resp$InvSimpson_scaled, alpha_resp$Respiration_scaled, method = "pearson")
## 
##  Pearson's product-moment correlation
## 
## data:  alpha_resp$InvSimpson_scaled and alpha_resp$Respiration_scaled
## t = -2.2565, df = 8, p-value = 0.05401
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
##  -0.899910986  0.009841998
## sample estimates:
##        cor 
## -0.6236489

0.8 Export all phyloseq object in one table

В табличке есть колонка cluster - “exl” в ней обозначает что это та часть датасета которая не пошла в WGCNA - мажоры в единичных семплах.

ps.m <- phyloseq::psmelt(ps.f)

ps.m <- ps.m %>% 
  mutate_if(is.character, as.factor) 

ps.data.out <- ps.m %>%
  select(-Group) %>% 
  pivot_wider(names_from = c(Day, Description, Sample), values_from = Abundance, values_fill = 0) 

#create empty dataframe with columnnames
external_empty_dataframe <- data.frame(OTU=factor(), cluster=factor(), stringsAsFactors = FALSE)

for (i in names(l_vst)) {
  a <- taxa_names(l_vst[[i]][["ps"]])
  b <- rep(i, length(a))
  d <- data.frame(OTU = as.factor(a),
                  cluster = as.factor(b))
  external_empty_dataframe <- rbind(external_empty_dataframe, d)
}

clusters.otu.df <- external_empty_dataframe
# add exl taxa -- taxa "exl"
d <- data.frame(OTU = as.factor(ps.exl.taxa),
                cluster = as.factor(rep("exl", length(ps.exl.taxa))))

clusters.otu.df <- rbind(clusters.otu.df, d)
ps.data.out.exl <- left_join(clusters.otu.df, ps.data.out, by="OTU")
# write.table(ps.data.out.exl, file = "ps.data.out.tsv", sep = "\t")
ps.data.out.exl

0.8.1 Несколько картинок по динамике предсталенности отдельных фил

Bdellovibrionota - хищники, индикатор развитого сообщества

ps.m %>% 
  filter(Phylum == "Bdellovibrionota") %>% 
  group_by(Description, Day) %>% 
  summarise(Bs = sum(Abundance)) %>% 
  ggplot() +
  geom_boxplot(aes(x = Day, y = Bs)) +
  theme_bw()
## `summarise()` has grouped output by 'Description'. You can override using the
## `.groups` argument.

Myxococcota - вроде бы тоже, но как нам известно могут быть целлулотитиками

ps.m %>% 
  filter(Phylum == "Myxococcota") %>% 
  group_by(Description, Day) %>% 
  summarise(Bs = sum(Abundance)) %>% 
  ggplot() +
  geom_boxplot(aes(x = Day, y = Bs)) +
  theme_bw()
## `summarise()` has grouped output by 'Description'. You can override using the
## `.groups` argument.

Археи появляются тоже на поздних стадиях - вообще я бы хотел бы опять развить тему важности азотного метаболизма на поздних стадиях разложения.
Оч хочется метагеном, но не этот.
Кроме того хочется отметить, что эти минорные группы возникают на D12

ps.m %>% 
  filter(Phylum == "Crenarchaeota") %>% 
  group_by(Description, Day) %>% 
  summarise(Bs = sum(Abundance)) %>% 
  ggplot() +
  geom_boxplot(aes(x = Day, y = Bs)) +
  theme_bw()
## `summarise()` has grouped output by 'Description'. You can override using the
## `.groups` argument.

Gammaproteobacteria - они треть кластера blue

ps.m %>% 
  filter(Class == "Gammaproteobacteria") %>% 
  group_by(Description, Day) %>% 
  summarise(Bs = sum(Abundance)) %>% 
  ggplot() +
  geom_boxplot(aes(x = Day, y = Bs)) +
  theme_bw()
## `summarise()` has grouped output by 'Description'. You can override using the
## `.groups` argument.

0.8.2 Боксплоты по филам

Все филы - представлененось логорифмирована по основанию 2
Отдельные точки - суммы абсолютных значений ридов по дням
Логорифмированы уже суммы, а не отдельные филотипы

#select only major phylums
top_phylum <- ps.m %>% 
  count(Phylum) %>% 
  arrange(desc(n)) %>% 
  top_n(10) %>% 
  pull(Phylum)
## Selecting by n
ps.m %>% 
  filter(Phylum %in% top_phylum) %>% 
  mutate(
    Phylum = as.character(Phylum),
    Class = as.character(Class),
    phylum = ifelse(Phylum == "Proteobacteria", Class, Phylum)
  ) %>% 
  group_by(Description, Day, phylum) %>% 
  filter(!is.na(phylum)) %>% 
  summarise(Bs = log2(sum(Abundance))) %>% 
  ggplot(aes(x = Day, y = Bs)) +
  geom_boxplot(fill="#4DBBD5B2", alpha=0.4) +
  theme_bw() +
  facet_wrap(~ phylum)
## `summarise()` has grouped output by 'Description', 'Day'. You can override
## using the `.groups` argument.
## Warning: Removed 46 rows containing non-finite values (stat_boxplot).

0.9 Добавим грибов

library(DESeq2)

ps_its <- readRDS("../../its/d2/ps_its")

amp_its <- phyloseq_to_ampvis2(ps_its)

ps.its.inall <- phyloseq::filter_taxa(ps_its, function(x) sum(x > 10) > (0.1*length(x)), TRUE)
ps.its.inall <- prune_taxa(taxa_sums(ps.its.inall) > 0, ps.its.inall)
Biostrings::writeXStringSet(ps.its.inall@refseq, file="ref_inall.fasta")
Biostrings::writeXStringSet(ps_its@refseq, file="ref.fasta")

tree <- ape::read.tree("../../its/d2/al.fasta.contree")

ps.its.inall@phy_tree <- tree
ps.its.inall  <- prune_taxa(taxa_sums(ps.its.inall) > 0, ps.its.inall)


ps.its.exl  <- phyloseq::filter_taxa(ps_its, function(x) sum(x > 10) < (0.1*length(x)), TRUE)
ps.its.exl  <- prune_taxa(taxa_sums(ps.its.exl) > 100, ps.its.exl)
ps.its.exl.taxa <- taxa_names(ps.its.exl)

ps.its.exl.taxa
##   [1] "Seq14"  "Seq34"  "Seq35"  "Seq38"  "Seq51"  "Seq55"  "Seq56"  "Seq57" 
##   [9] "Seq58"  "Seq60"  "Seq61"  "Seq64"  "Seq71"  "Seq72"  "Seq77"  "Seq80" 
##  [17] "Seq81"  "Seq82"  "Seq83"  "Seq84"  "Seq87"  "Seq88"  "Seq90"  "Seq95" 
##  [25] "Seq97"  "Seq98"  "Seq105" "Seq106" "Seq107" "Seq109" "Seq110" "Seq111"
##  [33] "Seq112" "Seq113" "Seq115" "Seq116" "Seq117" "Seq119" "Seq120" "Seq126"
##  [41] "Seq127" "Seq128" "Seq129" "Seq130" "Seq131" "Seq133" "Seq134" "Seq135"
##  [49] "Seq139" "Seq141" "Seq142" "Seq143" "Seq144" "Seq145" "Seq146" "Seq148"
##  [57] "Seq149" "Seq151" "Seq153" "Seq154" "Seq156" "Seq158" "Seq159" "Seq160"
##  [65] "Seq162" "Seq163" "Seq164" "Seq165" "Seq167" "Seq168" "Seq169" "Seq170"
##  [73] "Seq172" "Seq173" "Seq174" "Seq176" "Seq177" "Seq179" "Seq182" "Seq183"
##  [81] "Seq185" "Seq186" "Seq187" "Seq188" "Seq189" "Seq192" "Seq194" "Seq196"
##  [89] "Seq197" "Seq198" "Seq199" "Seq200" "Seq201" "Seq202" "Seq203" "Seq204"
##  [97] "Seq206" "Seq207" "Seq208" "Seq209" "Seq210" "Seq211" "Seq212" "Seq213"
## [105] "Seq214" "Seq216" "Seq217" "Seq218" "Seq219" "Seq220" "Seq221" "Seq222"
## [113] "Seq223" "Seq224" "Seq225" "Seq227" "Seq228" "Seq229" "Seq230" "Seq232"
## [121] "Seq233" "Seq234" "Seq236" "Seq237" "Seq238" "Seq239" "Seq240" "Seq241"
## [129] "Seq242" "Seq243" "Seq244" "Seq246" "Seq247" "Seq248" "Seq249" "Seq250"
## [137] "Seq251" "Seq252" "Seq253" "Seq255"
amp_its_inall <- phyloseq_to_ampvis2(ps.its.inall)

as.data.frame(ps_its@otu_table)
##                   Seq1 Seq2 Seq3 Seq4 Seq5 Seq6 Seq7 Seq8 Seq9 Seq10 Seq11
## straw-its2-D01-1     0    0    0    0    0 1297    0    0  831     0     0
## straw-its2-D01-2     0    0    0    0    0    0    0    0    0     0     0
## straw-its2-D01-3     0  883   27    0  630    0    0    0    0     0 11852
## straw-its2-D03-1     0    0 4212    0    0 1110    0  536    0     0     0
## straw-its2-D03-2     0    0 4432    0    0 1563    0 1697 2263     0     0
## straw-its2-D03-3     0    0 2453    0    0 2617    0 1245 2108     0     0
## straw-its2-D05-1     0    0 1188    0    0  117 2125  460    0     0     0
## straw-its2-D05-2     0    0 5819    0    0  721    0 1012    0     0     0
## straw-its2-D05-3     0    0 5416    0    0 2422    0  973 1298     0     0
## straw-its2-D05-4     0    0 5437    0    0  137 1415  960  298   365     0
## straw-its2-D05-5     0    0    0    0    0  881 1649  870 1009     0     0
## straw-its2-D07-1     0  122 2876 4674    0  788 5718 1666    0   113     0
## straw-its2-D07-2   920 5516 4192 4672 3760  660  546 2152 3012   428     0
## straw-its2-D07-3     0    0 3577  777    0  238 6781  559  674  1748   355
## straw-its2-D08-1    80    0  443  180  327  325 3435  915  804  3082     0
## straw-its2-D08-2  2024 3791   88 2126 2456  254    0    0    0     0     0
## straw-its2-D08-3     0    0 4113 7384    0   65  101 1972  690     0     0
## straw-its2-D10-1  3264    0 1825    0    0  585    0    0  579     0     0
## straw-its2-D10-2  6205  337 3298  574    0  848    0  596  949   164   180
## straw-its2-D10-3  2838    0  106 8478   29   74    0  182  193     0   145
## straw-its2-D10-4 10397 1098  672  279  792  476    0  372    0   404     0
## straw-its2-D10-5  7398    0    0  264    0    0    0    0 2219     0     0
## straw-its2-D12-1   208 5807    0 1756 3853  800    0  408  228   278     0
## straw-its2-D12-2  6419 5644  447   98 3533  210    0  744    0  1177   266
## straw-its2-D12-3  4376 1430  540 4655  908  686    0 1214    0   307   488
## straw-its2-D13-1  3955 2515  131    3 1367 1726    2  251  274    51     0
## straw-its2-D13-2  6832 3674    0 1532 2225  450  169    0  107    47     0
## straw-its2-D13-3  1742 4111  113  232 2091  512 1254    0  141   224     0
## straw-its2-D14-1     0 5289    0  279 3189 2223    0  161 1009     0    80
## straw-its2-D14-2  4258 4360  170 1330 2965  531    0  332    0  2667    98
## straw-its2-D14-3  4050  917   91 1596  629 2401    8  140   82   331     0
## straw-its2-D14-4  4912  332  159 1199  263  282 1640  363    0  2000     0
## straw-its2-D14-5  6765 3002  149  128 1785  607    0    0    0     0     0
## straw-its2-D15-1     0    0    0    0    0  104    0    0 1106     0  2520
## straw-its2-D15-2  4877 1088    0  260    0  758 1890  127    0  3162    62
## straw-its2-D15-3  2756 5628   41 1188 3492 1104    0    0    0     0     0
##                  Seq12 Seq13 Seq14 Seq15 Seq16 Seq17 Seq18 Seq19 Seq20 Seq21
## straw-its2-D01-1     0     0     0  3670     0     0     0     0  1680     0
## straw-its2-D01-2     0     0     0  8045     0     0     0     0     0     0
## straw-its2-D01-3     0     0     0     0     0     0     0     0   951     0
## straw-its2-D03-1     0     0     0   128     0     0     0     0   153     0
## straw-its2-D03-2     0     0     0     0     0     0     0     0  3556     0
## straw-its2-D03-3     0     0     0   701     0     0     0  2637   798     0
## straw-its2-D05-1     0  4797     0     0  1224     0     0     0     0     0
## straw-its2-D05-2     8     0     0     0     0     0     0  3091     0     0
## straw-its2-D05-3     0     0     0     0     0     0     0  2125     0     0
## straw-its2-D05-4     0     0     0     0   711     0     0  2553     0     0
## straw-its2-D05-5     0     0     0   151  1203     0     0     0     0     0
## straw-its2-D07-1     0     0     0     0  2438     0     0     0     0    35
## straw-its2-D07-2     0   655     0     0   236     0     0     0     0  1995
## straw-its2-D07-3     0     0     0     0  2614     0     0     6   563   128
## straw-its2-D08-1   130     0     0     0  1443     0     0     0   190   333
## straw-its2-D08-2     0     0     0     0     0     0     0     0     0  1623
## straw-its2-D08-3     0     0     0   125    46  3073     0     0   370     0
## straw-its2-D10-1   251  1581     0     0     0     0     0     0     0     0
## straw-its2-D10-2   614     0     0     0     0  4871     0     0     0     0
## straw-its2-D10-3     0     0     0     0     0     0    62     0   375   339
## straw-its2-D10-4     0  1632     0   118     0     0     0     0    99     0
## straw-its2-D10-5     0  3763     0    77     0     0     0     0     0   190
## straw-its2-D12-1   201     0     0   112     0     0   369     0     0     0
## straw-its2-D12-2   591     0     0     0     0     0     0     0     0   469
## straw-its2-D12-3    91     0     0     0     0     0     0     0     0   139
## straw-its2-D13-1   738     0     0   242     0     0  1942     0     0     0
## straw-its2-D13-2  1547   507     0     0     0     0   731     0    42   109
## straw-its2-D13-3   878     0     0     0  1075     0  1701     0     0    44
## straw-its2-D14-1  1191     0     0     0     0     0  3062     0     0   695
## straw-its2-D14-2    27     0     0     0     2     0     0     0     0  2102
## straw-its2-D14-3  2395     0     0     0     0     0  1317     0   184    43
## straw-its2-D14-4  2579     0     0     0   775     0  1487     0     0     0
## straw-its2-D14-5   362   854     0     0     0     0     0     0     0   638
## straw-its2-D15-1     0     0 13776     0     0     0     0     0   839     0
## straw-its2-D15-2  1666     0     0     0   978  2146   986     0     0     0
## straw-its2-D15-3   813     0     0     0     0  2563     0     0     0   661
##                  Seq22 Seq23 Seq24 Seq25 Seq26 Seq27 Seq28 Seq29 Seq30 Seq31
## straw-its2-D01-1     0  1620     0     0   157     0     0     0     0     0
## straw-its2-D01-2     0  1042     0     0     0     0     0     0     0     0
## straw-its2-D01-3     0  1782  1479     0     0     0     0     0     0  3310
## straw-its2-D03-1     0   929     0     0     0     0     0    18   873     0
## straw-its2-D03-2     0   998     0     0     0     0     0     0   748     0
## straw-its2-D03-3     0   368  1003     0  1009    58     0     0   644     0
## straw-its2-D05-1     0     0     0     0    30     0     0     0    35     0
## straw-its2-D05-2     0   143     0    71   191     0     0     0   588   326
## straw-its2-D05-3     0    10     0    32   277     0     0     0  1261     0
## straw-its2-D05-4   929     0     0     0   179     0     0     0   123     0
## straw-its2-D05-5     0     0   462     0   185     0     0     0   310     0
## straw-its2-D07-1     0     0     0  1902   210     0     0     0   121    10
## straw-its2-D07-2  1392    37   241     0   202    19     7     0    99     0
## straw-its2-D07-3   218    11   171     0   183    29     0     0     0     0
## straw-its2-D08-1   123    15     0   499     0     0     0     0     0     4
## straw-its2-D08-2     0     0   211     0     0     0     0     0     0     0
## straw-its2-D08-3  1209    23   327  1918   373     0     0     0     0     0
## straw-its2-D10-1     0     0     0     4     0     0     0     0   103     0
## straw-its2-D10-2     0     0     0     0  1045    20     0    60   301     0
## straw-its2-D10-3   338     0     0   241   156  3581   409     0     0     0
## straw-its2-D10-4   345     8     0     0   330     0     0     0    29     0
## straw-its2-D10-5   607     0     0     0     0     0   573     0     0     0
## straw-its2-D12-1     0    57  1044  1724   297     0     0   663     0     0
## straw-its2-D12-2     0     0     0     0   169    27     0   540     0     0
## straw-its2-D12-3  1127    64     0     0  1121     0     0     0     0     0
## straw-its2-D13-1     0    56     0   445   166     0     0   786     0    99
## straw-its2-D13-2     0     0     0     0   292     0     0   263     0     0
## straw-its2-D13-3     0     0    95   170     0  1057     0     0     0     0
## straw-its2-D14-1     0    27     0     0   328     0     0  1049     0    30
## straw-its2-D14-2     0     7     0     0   293     0     0     0     0     0
## straw-its2-D14-3     0     0     0   488   392     0  4543   270     0     0
## straw-its2-D14-4   785     0     0   746     0     0     0   624     0     0
## straw-its2-D14-5   989    10     0     0   122     0   968   292     0     0
## straw-its2-D15-1     0  1100  3010     0     0     0     0     0     0  1053
## straw-its2-D15-2   534     0   222     0   230     0     0  1082     7     0
## straw-its2-D15-3     0     0     0     0     0  2769     0     0     0     0
##                  Seq32 Seq33 Seq34 Seq35 Seq36 Seq37 Seq38 Seq39 Seq40 Seq41
## straw-its2-D01-1     0     0     0     0     0   955     0     0  1030     0
## straw-its2-D01-2     0     0     0     0     0   355     0     0  1320     0
## straw-its2-D01-3     0     0     0     0     0     0     0     0     0     0
## straw-its2-D03-1     0     0   593  1300     0    78   857     0   564  2184
## straw-its2-D03-2     0   879     0     0     0     0  1217     0   598     0
## straw-its2-D03-3     0     0  2004     0     0     0     0     0   459   937
## straw-its2-D05-1     0  1839     0  2588     0     0  2286     0     0     0
## straw-its2-D05-2     0   220     0     0     0   333     0     0     0     0
## straw-its2-D05-3     0  1608     0     0     0   198     0     0     0     0
## straw-its2-D05-4     0     0  1946     0     0    56     0     0    55     0
## straw-its2-D05-5     0     0     0     0     0     0     0     0     0     0
## straw-its2-D07-1     0     0     0     0     0    96     0     0     0     5
## straw-its2-D07-2    18     0     0     0     0     0     0   676     0     0
## straw-its2-D07-3   437     0     0     0     0     0     0   139    53     0
## straw-its2-D08-1     0     0     0     0    45  1118     0     0     0     0
## straw-its2-D08-2     0     0     0     0     4     0     0   740     0     0
## straw-its2-D08-3     0     0     0     0     0     0     0   389     0     0
## straw-its2-D10-1     0     0     0     0     0     0     0     0     0     0
## straw-its2-D10-2     0     0     0     0   123   289     0   280     0     0
## straw-its2-D10-3    38     0     0     0     0     0     0     0     0     0
## straw-its2-D10-4     0     0     0     0    84   114     0     0     0    47
## straw-its2-D10-5     0     0     0     0     0     0     0   311     0     0
## straw-its2-D12-1     0     0     0     0     0     0     0     0    97    53
## straw-its2-D12-2  1305     0     0     0   235   588     0     0     0     0
## straw-its2-D12-3   928     0     0   625   561     0     0   557     0   211
## straw-its2-D13-1     0     0     0     0   824     0     0     0     0   152
## straw-its2-D13-2   185     0     0     0   287    32     0     0     0     0
## straw-its2-D13-3   471     0     0     0   277     0     0     0     0     0
## straw-its2-D14-1     0     0     0     0    87     0     0     0     0    26
## straw-its2-D14-2   111     0     0     0     3     0     0     0     4   410
## straw-its2-D14-3     0     0     0     0  1148     0     0     0    16    68
## straw-its2-D14-4   646     0     0     0   160     0     0     0     0     0
## straw-its2-D14-5   514     0     0     0     0   204     0   859     0     0
## straw-its2-D15-1     0     0     0     0    17     0     0     0     0     0
## straw-its2-D15-2     0     0     0     0     0     0     0   397     0    91
## straw-its2-D15-3     0     0     0     0   574     0     0     0     0     0
##                  Seq42 Seq43 Seq44 Seq45 Seq46 Seq47 Seq48 Seq49 Seq50 Seq51
## straw-its2-D01-1     0     0     0   653     0   401     0     0     0     0
## straw-its2-D01-2     0     0     0   537     0     0     0     0     0     0
## straw-its2-D01-3     0     0     0   779   285     0     0     0     0     0
## straw-its2-D03-1     0  1383     0     0     0     0     0     0     0     0
## straw-its2-D03-2     0   300     0     0     0  1162     0     0     0     0
## straw-its2-D03-3     0  1107     0   400     0     0     0     0     0     0
## straw-its2-D05-1   336     0     0     0     0     0     0   279     0     0
## straw-its2-D05-2     0   118     0    41     0     0     0     0   289     0
## straw-its2-D05-3     0   440     0     0     0     0     0     0     0     0
## straw-its2-D05-4   213   147     0     0     0     0     0   197     0     0
## straw-its2-D05-5   287   522     0   127     0     0     0   316     0     0
## straw-its2-D07-1   768     0     0    26     0     0     0   585   392     0
## straw-its2-D07-2   107     0    11     0     0     0     4     0    62     0
## straw-its2-D07-3   878     0   306     0     0     0   315   709   326     0
## straw-its2-D08-1   495     0     0     0   176     0     0   334   464     0
## straw-its2-D08-2     0     0     0     0     0     0     0     0     0     0
## straw-its2-D08-3     0     0     0     0     0     0     0     0   249     0
## straw-its2-D10-1     0     0     0     0     0     0     0     0     0     0
## straw-its2-D10-2     0     0     0   104   176     0     0     0     0     0
## straw-its2-D10-3     0     0    42    30     0   402     0     0    56     0
## straw-its2-D10-4     0     0    11   118     0     0     0     0     0     0
## straw-its2-D10-5     0     0     0   134     0   199    11     0     0     0
## straw-its2-D12-1     0     0     0   169     0     0     0     0   379     0
## straw-its2-D12-2     0     0   715     0     0   238   806     0     0     0
## straw-its2-D12-3     0     0   814   133    79   791   622     0   146     0
## straw-its2-D13-1     0     0     0     0     0     0     0     0     0  2875
## straw-its2-D13-2     0     0   218    30     0     0   200     0     0     0
## straw-its2-D13-3   267     0   354     0  1241     0   422   341   164     0
## straw-its2-D14-1     0     0     0    73   429   236     0     0   295     0
## straw-its2-D14-2     0     0   110     0     0     0   132     0     0     0
## straw-its2-D14-3     0     0   322     0   426     0   273     0     0     0
## straw-its2-D14-4   399     0   494     0     0     0   389     0   181     0
## straw-its2-D14-5     0     0   336     0     0     0     0     0     0     0
## straw-its2-D15-1     0     0     0   197     0     0     0     0     0     0
## straw-its2-D15-2   285     0     0     0     0     0     0   254     0     0
## straw-its2-D15-3     0     0     0     0   704     0     0     0     0     0
##                  Seq52 Seq53 Seq54 Seq55 Seq56 Seq57 Seq58 Seq59 Seq60 Seq61
## straw-its2-D01-1     0     0     0     0     0     0     0     0     0     0
## straw-its2-D01-2     0     0     0     0     0     0     0     0     0     0
## straw-its2-D01-3     0     0     0     0     0     0  2297     0     0     0
## straw-its2-D03-1   343   100     0     0     0     0     0    99     0     0
## straw-its2-D03-2     0     0     0     0  2314     0     0     0     0     0
## straw-its2-D03-3   490   437     0     0     0     0     0     0     0     0
## straw-its2-D05-1     0     0     0     0     0     0     0     0  1334     0
## straw-its2-D05-2     0   479     0     0     0     0     0     0     0  2180
## straw-its2-D05-3   963   659     0     0     0     0     0     0     0     0
## straw-its2-D05-4     0   163   284     0     0     0     0   548     0     0
## straw-its2-D05-5   718   276     0  2321     0  2313     0     0     0     0
## straw-its2-D07-1    52   114   643     0     0     0     0     0     0     0
## straw-its2-D07-2     0     0   177     0     0     0     0    19     0     0
## straw-its2-D07-3     0    32     0     0     0     0     0     0     0     0
## straw-its2-D08-1     0     0  1253     0     0     0     0     0     0     0
## straw-its2-D08-2     0     0     0     0     0     0     0     0     0     0
## straw-its2-D08-3     0   154     0     0     0     0     0   440     0     0
## straw-its2-D10-1     0     0     0     0     0     0     0   269     0     0
## straw-its2-D10-2     0   193     0     0     0     0     0     0     0     0
## straw-its2-D10-3     0     0     0     0     0     0     0     0     0     0
## straw-its2-D10-4     0     0     0     0     0     0     0     0   439     0
## straw-its2-D10-5    35     0     0     0     0     0     0     0     0     0
## straw-its2-D12-1     0     0    43     0     0     0     0     0     0     0
## straw-its2-D12-2     0     0    53     0     0     0     0    31     0     0
## straw-its2-D12-3    15     0     0     0     0     0     0   637     0     0
## straw-its2-D13-1    19     0     0     0     0     0     0     0     0     0
## straw-its2-D13-2     0     0     0     0     0     0     0     0     0     0
## straw-its2-D13-3     0     0     0     0     0     0     0     0     0     0
## straw-its2-D14-1     0     0     0     0     0     0     0     0     0     0
## straw-its2-D14-2     0     0     0     0     0     0     0     0     0     0
## straw-its2-D14-3     0     0     0     0     0     0     0     0     0     0
## straw-its2-D14-4     0     0     0     0     0     0     0     0     0     0
## straw-its2-D14-5     0     0     0     0     0     0     0     0   431     0
## straw-its2-D15-1     0     0     0     0     0     0     0    99     0     0
## straw-its2-D15-2     0     0     0     0     0     0     0    35     0     0
## straw-its2-D15-3     0     0     0     0     0     0     0    31     0     0
##                  Seq62 Seq63 Seq64 Seq65 Seq66 Seq67 Seq68 Seq69 Seq70 Seq71
## straw-its2-D01-1     0   846     0     0     0     0     0     0   105     0
## straw-its2-D01-2     0     0     0     0     0     0     0     0     0     0
## straw-its2-D01-3     0     0     0     0     0     0     0     0     0     0
## straw-its2-D03-1     0   629     0     0     0     0   154     0   159     0
## straw-its2-D03-2     0   493     0     0     0     0   116   556     0     0
## straw-its2-D03-3     0     0     0     0     0     0    39     0    94     0
## straw-its2-D05-1     0     0     0     0    73     0    16    24     0     0
## straw-its2-D05-2     0     0     0     0   505     0   785   147     0     0
## straw-its2-D05-3     0    18     0     0     0     0   385   106     0     0
## straw-its2-D05-4     0     0     0     0     0     0   381    22     0     0
## straw-its2-D05-5     0    61     0     0     0     0     9     0   106     0
## straw-its2-D07-1     0     0     0  1255   824     0     0    67     0     0
## straw-its2-D07-2     0    67     0     0     0     0     0     0     0     0
## straw-its2-D07-3   234     0     0     0     0     0     0     0     0     0
## straw-its2-D08-1     0     0     0     0     0     0     2   406     0     0
## straw-its2-D08-2     0     0     0    90     0     0     3     0    71     0
## straw-its2-D08-3     0     0     0     0     0     0     5     0     0     0
## straw-its2-D10-1     0     0  2127     0     0   608     0     0     0     0
## straw-its2-D10-2     0     0     0     0     0     0     7     0     0     0
## straw-its2-D10-3    16     0     0     0     0     0     0     0     0     0
## straw-its2-D10-4     0     0     0     0   436     0     0     0     0  1703
## straw-its2-D10-5    21     0     0     0     0    34     0     0     0     0
## straw-its2-D12-1     0     0     0     0     0   957     2   228   502     0
## straw-its2-D12-2   588    30     0     0    10     0     0     0     0     0
## straw-its2-D12-3   486     0     0   238     0     0     0     0   372     0
## straw-its2-D13-1     0     0     0     0     0     0     0     0   356     0
## straw-its2-D13-2   111     0     0     0     0     0     0     0     0     0
## straw-its2-D13-3     0     0     0    27     0    85     0     0     0     0
## straw-its2-D14-1     0     0     0     0     0     0     0     0     0     0
## straw-its2-D14-2    74     0     0   431     0     0     0     0     0     0
## straw-its2-D14-3   176     0     0     0     0     0     0   190     0     0
## straw-its2-D14-4   278     0     0     0     0     0     0    34     0     0
## straw-its2-D14-5   193     0     0     0   132     0     0    60     0     0
## straw-its2-D15-1     0     0     0     0     0   232     0     0     0     0
## straw-its2-D15-2     0     0     0    21    37     0     0     0     0     0
## straw-its2-D15-3     0     0     0     0    17     0     0    49     0     0
##                  Seq72 Seq73 Seq74 Seq75 Seq76 Seq77 Seq78 Seq79 Seq80 Seq81
## straw-its2-D01-1     0     0     0     0     0     0     0     0     0     0
## straw-its2-D01-2     0     0     0     0     0     0     0     2  1358     0
## straw-its2-D01-3     0     0     0     2     0     0     0     1     0     0
## straw-its2-D03-1     0     0     0     0     0     0     0   100     0     0
## straw-its2-D03-2     0     0     0     7     0     0     0    95     0     0
## straw-its2-D03-3     0     0     0     0     0     0     0    40     0     0
## straw-its2-D05-1     0     0     0   136     0     0     0    53     0     0
## straw-its2-D05-2     0     0     0    17     0     0     0   403     0     0
## straw-its2-D05-3     0     0     0     8     0  1534     0   268     0     0
## straw-its2-D05-4     0     0     0   986     0     0     0   153     0     0
## straw-its2-D05-5  1656     0     0     2     0     0     0   205     0     0
## straw-its2-D07-1     0     0     0     0     0     0     0     0     0   263
## straw-its2-D07-2     0     0     0     0     0     0     0     9     0   408
## straw-its2-D07-3     0     0     0     0    63     0     0     0     0     0
## straw-its2-D08-1     0     0   129     8   127     0     0     0     0     0
## straw-its2-D08-2     0     0   299     0     0     0     0     0     0     0
## straw-its2-D08-3     0     0     0     5     0     0     0     6     0     0
## straw-its2-D10-1     0    57     0    61     0     0     0     2     0     0
## straw-its2-D10-2     0   277     0    95   176     0     0    13     0     5
## straw-its2-D10-3     0     0     0     0     0     0    21     0     0     0
## straw-its2-D10-4     0     0     0     0    97     0     0     6     0     0
## straw-its2-D10-5     0    24     0     0     0     0    30     0     0     0
## straw-its2-D12-1     0    38     0    42     0     0     0     0     0     0
## straw-its2-D12-2     0   146   415    13     0     0     0     0     0     0
## straw-its2-D12-3     0    58     0    41     0     0   518     4     0     0
## straw-its2-D13-1     0   207     0    18     0     0     0     0     0     0
## straw-its2-D13-2     0     0    22     9     0     0   105     2     0     0
## straw-its2-D13-3     0     0     0     5     0     0     0     0     0     0
## straw-its2-D14-1     0     0     0    13   648     0     0     0     0     0
## straw-its2-D14-2     0   145   392     0     0     0    98     0     0     0
## straw-its2-D14-3     0   136     0    25   222     0   187     0     0     0
## straw-its2-D14-4     0     0     0    33     0     0   335     0     0     0
## straw-its2-D14-5     0   335     0    20     0     0   240     0     0     0
## straw-its2-D15-1     0     0     0    39     0     0     0     0     0     0
## straw-its2-D15-2     0    79   286     0   110     0     0     0     0     0
## straw-its2-D15-3     0   103    57     0   120     0     0     0     0   661
##                  Seq82 Seq83 Seq84 Seq85 Seq86 Seq87 Seq88 Seq89 Seq90 Seq91
## straw-its2-D01-1     0     0     0     0     0     0     0     0   366     0
## straw-its2-D01-2     0     0     0     0     0     0     0     0     0     0
## straw-its2-D01-3     0     0     0     0     0     0     0     0     0     0
## straw-its2-D03-1     0     0     0     0     0     0     0     0     0     0
## straw-its2-D03-2     0     0     0     0     0     0     0     0   724     0
## straw-its2-D03-3     0     0     0     0     0     0     0     0     0     0
## straw-its2-D05-1     0     0     0     0    97     0     0     0     0     0
## straw-its2-D05-2     0  1242     0     0     0     0     0     0     0     0
## straw-its2-D05-3     0     0     0     0     0     0     0     0     0     0
## straw-its2-D05-4     0     0     0     0    70     0     0     0     0     0
## straw-its2-D05-5     0     0     0     0    86  1166     0     0     0     0
## straw-its2-D07-1     0     0     0     0   247     0     0     0     0     0
## straw-its2-D07-2     0     0     0    12    25     0     0    84     0     0
## straw-its2-D07-3  1273     0     0   244   284     0     0   656     0     0
## straw-its2-D08-1     0     0     0     0   148     0     0     0     0     0
## straw-its2-D08-2     0     0     0     0     0     0     0     0     0   552
## straw-its2-D08-3     0     0     0     0     0     0     0     0     0     0
## straw-its2-D10-1     0     0     0     0     0     0     0     0     0     0
## straw-its2-D10-2     0     0     0     0     0     0     0   118     0     0
## straw-its2-D10-3     0     0     0     0     0     0     0     0     0   292
## straw-its2-D10-4     0     0     0     0     0     0     0     0     0     0
## straw-its2-D10-5     0     0     0     0     0     0  1106     0     0     0
## straw-its2-D12-1     0     0     0     0     0     0     0     0     0     0
## straw-its2-D12-2     0     0     0   672     0     0     0     0     0     0
## straw-its2-D12-3     0     0     0     0     0     0     0     0     0     0
## straw-its2-D13-1     0     0  1235     0     0     0     0     0     0     0
## straw-its2-D13-2     0     0     0     0     0     0     0    20     0     0
## straw-its2-D13-3     0     0     0   290    76     0     0     0     0     0
## straw-its2-D14-1     0     0     0     0     0     0     0   226     0     0
## straw-its2-D14-2     0     0     0     0     0     0     0     0     0     0
## straw-its2-D14-3     0     0     0     0     0     0     0     0     0     0
## straw-its2-D14-4     0     0     0     0    61     0     0     0     0     0
## straw-its2-D14-5     0     0     0     0     0     0     0     0     0    86
## straw-its2-D15-1     0     0     0     0     0     0     0     0     0     0
## straw-its2-D15-2     0     0     0     0    88     0     0     0     0     0
## straw-its2-D15-3     0     0     0     0     0     0     0     0     0   134
##                  Seq92 Seq93 Seq94 Seq95 Seq96 Seq97 Seq98 Seq99 Seq100 Seq101
## straw-its2-D01-1     0     0     0   409     0     0   951     0    224      0
## straw-its2-D01-2     0     0     0     0     0     0     0     0      0      0
## straw-its2-D01-3     0     0     0   607     0     0     0     0      0      0
## straw-its2-D03-1     0     0     0     0   141     0     0    24     82     37
## straw-its2-D03-2     0     0     0     0   213     0     0    24    293      0
## straw-its2-D03-3     0     0     0     8    14     0     0     3      0      0
## straw-its2-D05-1    72     0     0     0     0     7     0     4      0      0
## straw-its2-D05-2     0     0     0     0   521     0     0   412     45      0
## straw-its2-D05-3     0     0     0     0   132     0     0     0     60      0
## straw-its2-D05-4     0     0     0     0     0     0     0   396     25      0
## straw-its2-D05-5     0     0     0     0     0     0     0    42      0      0
## straw-its2-D07-1   338    25     0     0     0     0     0     0      0      0
## straw-its2-D07-2    24     0     0     0     0   112     0     0      0      0
## straw-its2-D07-3   414    89     0     0     0     0     0     0      0      0
## straw-its2-D08-1   210   150     0     0     0     0     0     2      0      0
## straw-its2-D08-2     0     0     0     0     0     0     0     0      0      0
## straw-its2-D08-3     0   125     0     0     0     0     0     0     48      0
## straw-its2-D10-1     0     0     0     0     0     0     0    20      0      0
## straw-its2-D10-2     0    17    34     1     0     0     0    13      0     33
## straw-its2-D10-3     0     0     0     0     0     0     0     0      0      0
## straw-its2-D10-4     0    27     0     0     0     0     0     1      0     32
## straw-its2-D10-5     0     0     0     0     0     0     0     0      0      5
## straw-its2-D12-1     0   113    32     0     0     0     0     0      0    454
## straw-its2-D12-2     0     0   111     3     0     0     0     3     94     34
## straw-its2-D12-3     0   112     0     0     0     0     0     0      0     21
## straw-its2-D13-1     0     0   162     0     0     0     0     0      0    110
## straw-its2-D13-2     0     0     0     0     0     0     0     0      0      0
## straw-its2-D13-3     0     0    64     0     0     0     0     0      0     36
## straw-its2-D14-1     0     0   128     0     0     0     0     0      0      0
## straw-its2-D14-2     0    38     0     0     0     0     0     0      0      0
## straw-its2-D14-3     0    95     0     0     0     0     0     0      0     54
## straw-its2-D14-4     0   202   147     0     0   847     0     1      0     13
## straw-its2-D14-5     0     7   142     0     0     0     0     0     41      0
## straw-its2-D15-1     0     0     0     0     0     0     0     0      0     80
## straw-its2-D15-2     0    30   220     0     0     0     0     0      0      0
## straw-its2-D15-3     0    10     0     0     0     0     0     0     18     15
##                  Seq102 Seq103 Seq104 Seq105 Seq106 Seq107 Seq108 Seq109 Seq110
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      3      0      0    874      0    839      0      0      0
## straw-its2-D03-1     20      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      5      0      0      0      0      0      0      0      0
## straw-its2-D05-1    130      0      9      0      0      0      0      0      0
## straw-its2-D05-2    139      0      0      0      0      0      0      0      0
## straw-its2-D05-3      5      0      0      0      0      0      0      0      0
## straw-its2-D05-4    231      0      0      0    715      0      0      0      0
## straw-its2-D05-5      3      0      0      0    127      0      0      0      0
## straw-its2-D07-1      0      0     16      0      0      0      0      0      0
## straw-its2-D07-2      0      8      0      0      0      0      2      0      0
## straw-its2-D07-3      0    182    159      0      0      0     86      0    797
## straw-its2-D08-1      6      0    241      0      0      0      0      0      0
## straw-its2-D08-2      5      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0     60      0      0
## straw-its2-D10-1      8      0      0      0      0      0      0      0      0
## straw-its2-D10-2    163      0    213      0      0      0    106      0      0
## straw-its2-D10-3     24     18     33      0      0      0      0      0      0
## straw-its2-D10-4     12      0    116      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      7      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0     70     10      0      0      0    165      0      0
## straw-its2-D12-3      0      0      0      0      0      0    119    529      0
## straw-its2-D13-1      7      0      0      0      0      0      0      0      0
## straw-its2-D13-2      3    104      0      0      0      0      0      0      0
## straw-its2-D13-3      0    236      0      0      0      0     81      0      0
## straw-its2-D14-1     14      0      0      0      0      0      0      0      0
## straw-its2-D14-2      8      0      0      0      0      0     21     82      0
## straw-its2-D14-3      8      0     38      0      0      0      0    196      0
## straw-its2-D14-4      9     38      6      0      0      0     85      0      0
## straw-its2-D14-5     36    244     27      0      0      0      0      0      0
## straw-its2-D15-1     59      0      0      0      0      0      0      0      0
## straw-its2-D15-2     12      0      0      0      0      0     40      0      0
## straw-its2-D15-3      6      0     17      0      0      0     39      0      0
##                  Seq111 Seq112 Seq113 Seq114 Seq115 Seq116 Seq117 Seq118 Seq119
## straw-its2-D01-1      0      0      0      0      0    316      0      0    614
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0    775      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0    103
## straw-its2-D03-2      0      0      0      0      0      0    740      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0    432      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0    168      0      0      0      0      0
## straw-its2-D07-2      0    796      0     21      0      0      0      0      0
## straw-its2-D07-3      0      0      0    443      0      0      0     34      0
## straw-its2-D08-1      0      0      0     95      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0     47      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0     14      0
## straw-its2-D12-1    797      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0    418      0
## straw-its2-D12-3      0      0      0      0    474      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0    288      0      0    257      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq120 Seq121 Seq122 Seq123 Seq124 Seq125 Seq126 Seq127 Seq128
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      9      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0    283      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0    463      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0    287      0     92    660      0      0
## straw-its2-D05-4      0     45      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0     44      0      0     49      0      0      0     48
## straw-its2-D07-3      0      0      3      0      0      0      0      0    561
## straw-its2-D08-1      0     91      0      0      0    363      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0     11      0      0      0      0
## straw-its2-D10-1      0      0      0      0    423      0      0      0      0
## straw-its2-D10-2      0      0      8      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0     12     32      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0     43      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0     90      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0    198      0    148     87      0      0      0
## straw-its2-D13-3      0      0    259      0      0      0      0      0      0
## straw-its2-D14-1      0      0     48      0      0     10      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0     20      0      0      0      0      0      0
## straw-its2-D14-4      0      0     93      0      0     77      0      0      0
## straw-its2-D14-5    701      0      0      0      0     32      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0     39      0      0      0      0    622      0
##                  Seq129 Seq130 Seq131 Seq132 Seq133 Seq134 Seq135 Seq136 Seq137
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      8      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0    520      0      0      0     40
## straw-its2-D05-1      0      0      0    342      0      0      0      0    136
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0    570      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      7      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0    213    268
## straw-its2-D08-1      0      0      0      3      0      0      0     18      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0     52      0
## straw-its2-D10-1      0      0    552     61      0      0      0      0      0
## straw-its2-D10-2      0      0      0      4      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0     58      0
## straw-its2-D10-5      0      0      0      2      0      0    504      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0     38      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0     23      0      0      0      0      0
## straw-its2-D13-2     58      0      0     11      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0     56
## straw-its2-D14-1    382      0      0     40      0      0      0      0      0
## straw-its2-D14-2    168      0      0      1      0    310      0     65      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0     26      0    207      0      0      0
## straw-its2-D14-5      0      0      0      1      0      0      0     58      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq138 Seq139 Seq140 Seq141 Seq142 Seq143 Seq144 Seq145 Seq146
## straw-its2-D01-1      0      0      8      0      0      0      0      0    415
## straw-its2-D01-2      0      0      0      0      0      0      0    446      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0    105      0     88      0      0      0      0
## straw-its2-D03-2      9      0     21      0      0      0      0      0      0
## straw-its2-D03-3      0      0     13      0      0      0      0      0      0
## straw-its2-D05-1      0      0      4      0      0      0      0      0      0
## straw-its2-D05-2    200      0      2      0      0      0      0      0      0
## straw-its2-D05-3      0      0      4      0      0      0      0      0      0
## straw-its2-D05-4    210      0     84      0      0      0      0      0      0
## straw-its2-D05-5     24      0      0    470      0      0      0      0      0
## straw-its2-D07-1      0      0      4      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0     16      0    372      0      0      0      0
## straw-its2-D08-3      5      0      2      0      0      0      0      0      0
## straw-its2-D10-1     17      0    170      0      0      0      0      0      0
## straw-its2-D10-2     10      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      5      0      0      0      0      0      0
## straw-its2-D10-4      0    472      3      0      0      0    448      0      0
## straw-its2-D10-5      0      0      3      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      2      0      0      0      0      0      0
## straw-its2-D12-3      0      0      1      0      0      0      0      0      0
## straw-its2-D13-1      0      0      4      0      0      0      0      0      0
## straw-its2-D13-2      0      0     19      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0    457      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      1      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq147 Seq148 Seq149 Seq150 Seq151 Seq152 Seq153 Seq154 Seq155
## straw-its2-D01-1      0      0      0      4      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      3
## straw-its2-D03-1    128      0      0     17      0      0      0      0      0
## straw-its2-D03-2    132      0      0      4      0     19      0      0      0
## straw-its2-D03-3      0      0    400      8      0     65      0      0      0
## straw-its2-D05-1      0      0      0      3      0      1      0      0      0
## straw-its2-D05-2     80      0      0      0      0     59      0      0      0
## straw-its2-D05-3     68      0      0     72      0     11      0      0      0
## straw-its2-D05-4      0      0      0      5      0    102      0      6      0
## straw-its2-D05-5      0      0      0      0      0     42      0      0      0
## straw-its2-D07-1      0      0      0     16      0      0      0      0      0
## straw-its2-D07-2      0      0      0     13      0      0      0    106      0
## straw-its2-D07-3      0      0      0      0    393      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0     29      0    202      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      3
## straw-its2-D10-2      0      0      0     12      0      6      0      0      4
## straw-its2-D10-3      0      0      0      5      0     11      0      0      0
## straw-its2-D10-4      0      0      0      0      0     36      0      0      1
## straw-its2-D10-5      0      0      0      0      0      1      0      0      1
## straw-its2-D12-1      0      0      0     11      0      0      0      0     57
## straw-its2-D12-2      0      0      0      0      0      0      0      0     34
## straw-its2-D12-3      0      0      0     66      0      3      0     68     25
## straw-its2-D13-1      0      0      0      0      0      0    385      0     29
## straw-its2-D13-2      0      0      0      0      0      0      0      0     69
## straw-its2-D13-3      0      0      0      0      0      0      0      0      8
## straw-its2-D14-1      0      0      0     57      0      0      0      0     16
## straw-its2-D14-2      0      0      0     27      0      0      0      0     17
## straw-its2-D14-3      0      0      0     35      0      0      0      0     34
## straw-its2-D14-4      0    407      0      0      0      4      0      0      8
## straw-its2-D14-5      0      0      0      0      0      2      0      0     16
## straw-its2-D15-1      0      0      0     12      0      0      0      0     14
## straw-its2-D15-2      0      0      0      8      0      0      0      0     25
## straw-its2-D15-3      0      0      0     20      0      0      0      0     16
##                  Seq156 Seq157 Seq158 Seq159 Seq160 Seq161 Seq162 Seq163 Seq164
## straw-its2-D01-1      0      0    349      0      0    198      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      7      0      0     58      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      1      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0     18      0      0      0
## straw-its2-D05-2      0    144      0      0      0      6      0      0      0
## straw-its2-D05-3      0      0      0    357      0     53      0      0      0
## straw-its2-D05-4      0      0      0      0      0      9      0      0      0
## straw-its2-D05-5      0      0      3      0      0      0      0      0      0
## straw-its2-D07-1    376      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0     72      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      6      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      4
## straw-its2-D10-4      0    124      0      0      0      0      0      0      7
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0    343    338      0
## straw-its2-D13-2      0      0      0      0      0      2      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0     25      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0    356      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0    314
## straw-its2-D15-1      0      0      0      0      0      0      0      0      6
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq165 Seq166 Seq167 Seq168 Seq169 Seq170 Seq171 Seq172 Seq173
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0    129      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0     58      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0     13      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0     15      0      0
## straw-its2-D07-2      0      0      0      0      0    287      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0    128      0      0      0      0      0      0
## straw-its2-D10-2      0     50      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0     68      0      0
## straw-its2-D10-4      0      0      0      0      0      0     38      0    298
## straw-its2-D10-5      0    108      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0     57      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0    301      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0     81      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1    322      9      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0     38      0      0      0      0    122    300      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0    302      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0     31      0      0      0      0      0      0      0
##                  Seq174 Seq175 Seq176 Seq177 Seq178 Seq179 Seq180 Seq181 Seq182
## straw-its2-D01-1    297    177      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      2    147      0
## straw-its2-D03-1      0      0      0      0      0      0      0     89      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0     61      0      0      0      0      0     11      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0    293      0      0      0    173      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      5      0      0
## straw-its2-D05-5      0      0      0      0      0    285      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0     39      0      0      0      0      0     28      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0     25      0    274
## straw-its2-D08-3      0      0      0      0      0      0      2      0      0
## straw-its2-D10-1      0      0      0    291    186      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0     58      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0     15      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0     19      0      1      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0     25      0      0      1      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      7      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      1      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0     17      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0     50      0      0
##                  Seq183 Seq184 Seq185 Seq186 Seq187 Seq188 Seq189 Seq190 Seq191
## straw-its2-D01-1      8      0      0      0      0      0      0      0      0
## straw-its2-D01-2    216      0      0      0      0      0      0      0      0
## straw-its2-D01-3     30      1      0      0    254      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      5      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      3      0      0      0      0      0      0      0      0
## straw-its2-D05-4      1      1      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      1      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      2      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      4     34      0      0      0      0      0     25     26
## straw-its2-D10-2      2     23      0      0      0      0    248      9     62
## straw-its2-D10-3      0     46      0      0      0      0      0     14      5
## straw-its2-D10-4      0     15      0      0      0      0      0     30     43
## straw-its2-D10-5      0      0    263      0      0      0      0     77      5
## straw-its2-D12-1      0     12      0      0      0      0      0      0      0
## straw-its2-D12-2      0     37      0      0      0      0      0      0      7
## straw-its2-D12-3      0     63      0      0      0      0      0      6     57
## straw-its2-D13-1      0      0      0    255      0      0      0      2      0
## straw-its2-D13-2      0     13      0      0      0      0      0      1     21
## straw-its2-D13-3      0      0      0      0      0    254      0      2      3
## straw-its2-D14-1      0      4      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0     11      3
## straw-its2-D14-3      1      9      0      0      0      0      0      6      1
## straw-its2-D14-4      0      0      0      0      0      0      0     15     11
## straw-its2-D14-5      0      0      0      0      0      0      0     35      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      2      0      0      0      0      0      0      8      0
## straw-its2-D15-3      0      6      0      0      0      0      0      2      1
##                  Seq192 Seq193 Seq194 Seq195 Seq196 Seq197 Seq198 Seq199 Seq200
## straw-its2-D01-1      0     31      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3    244      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0     88      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      6      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0     88      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      2      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0     13      0      0      0      0      0
## straw-its2-D08-2      0      0      0      3      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0    238      2      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0     10    219      0      0      0      0
## straw-its2-D12-1      0      9      0      1      0      0      0      0      0
## straw-its2-D12-2      0      0      0     16      0      0      0      0      0
## straw-its2-D12-3      0      2      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0     53      0      0      0      0      0
## straw-its2-D13-2      0      0      0     39      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0     15      0      0      0    207      0      0      0
## straw-its2-D14-2      0      0      0     72      0      0      0      0      0
## straw-its2-D14-3      0      4      0      0      0      0    204      0      0
## straw-its2-D14-4      0      0      0      6      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      1      0      0      0      0    196
## straw-its2-D15-2      0      2      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      1      0      0      0    201      0
##                  Seq201 Seq202 Seq203 Seq204 Seq205 Seq206 Seq207 Seq208 Seq209
## straw-its2-D01-1      0      0      0      0     85      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0    191    187      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0     56      0      0      0    175
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2     52      0      0      0      0      0      0      0      0
## straw-its2-D05-3    140      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0    178      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      2      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0    179      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0     18      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0    180      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0     24      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0    186      0      0      0      0      0
##                  Seq210 Seq211 Seq212 Seq213 Seq214 Seq215 Seq216 Seq217 Seq218
## straw-its2-D01-1    170      0      0      0      0      7      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0    170      0      0      0     14      0      0      0
## straw-its2-D03-2      0      0      0      0      0     43      0      0      0
## straw-its2-D03-3      0      0      0      0      0      6      0      0      0
## straw-its2-D05-1      0      0      0      0      0      3      0      0      0
## straw-its2-D05-2      0      0    164      0      0     31      0    147      0
## straw-its2-D05-3      0      0      0      0      0     23      0      0      0
## straw-its2-D05-4      0      0      0      0      9      0      0      0    145
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0    101      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0    155      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      5      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      3      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0    163      1      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0     43      2      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      2      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      3      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      3      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      3     20      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq219 Seq220 Seq221 Seq222 Seq223 Seq224 Seq225 Seq226 Seq227
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      7      0      0      0    138      0      0      0
## straw-its2-D03-2      0      2      0      0      0      0      0      0      0
## straw-its2-D03-3      0      1      0      0      0      0      0      0      0
## straw-its2-D05-1      0      9      0      0      0      0     14      0      0
## straw-its2-D05-2      0      1      0      0      0      0      4      0      0
## straw-its2-D05-3      0      4      0    141      0      0      3      0      0
## straw-its2-D05-4      0     55      0      0      0      0     46      0      0
## straw-its2-D05-5      0      1      0      0      0      0      1      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0     73      0
## straw-its2-D07-3      0      0      0      0    141      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      3      0      0
## straw-its2-D10-1      0      7      0      0      0      0      6      0      0
## straw-its2-D10-2      0     23      0      0      0      0     35      0      0
## straw-its2-D10-3      0      5      0      0      0      0      1      0      0
## straw-its2-D10-4    145      0      0      0      0      0      1      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      2      0      0      0      0      0      0      0
## straw-its2-D12-2      0      6      0      0      0      0      1      0      0
## straw-its2-D12-3      0      4      0      0      0      0      2      0    135
## straw-its2-D13-1      0      1      0      0      0      0      1     25      0
## straw-its2-D13-2      0      1      0      0      0      0      1      0      0
## straw-its2-D13-3      0      1      0      0      0      0      2      0      0
## straw-its2-D14-1      0      3      0      0      0      0      3     19      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      3      0      0      0      0      2      0      0
## straw-its2-D14-4      0      1      0      0      0      0      1      0      0
## straw-its2-D14-5      0      4      0      0      0      0      3      0      0
## straw-its2-D15-1      0      3      0      0      0      0      4     18      0
## straw-its2-D15-2      0      0    142      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      1      0      0
##                  Seq228 Seq229 Seq230 Seq231 Seq232 Seq233 Seq234 Seq235 Seq236
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0     15      0
## straw-its2-D03-1      0      0      0      0      0      0    122      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0    110      5      0      0      0
## straw-its2-D05-3      0      0      0      0      0     59      0      0      0
## straw-its2-D05-4      0      0      0      0      4      3      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      4      0      0     17      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2     98      0      0      8      0     26      0      1      0
## straw-its2-D10-3      0      0     91      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0     15      5      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      1      0
## straw-its2-D12-1      0      0      0      4      0      6      0      8      0
## straw-its2-D12-2     35      0      0      0      0      0      0      1      0
## straw-its2-D12-3      0      0      0     30      0      0      0      3      0
## straw-its2-D13-1      0    131      0     14      0      0      0     15      0
## straw-its2-D13-2      0      0      0      0      0      0      0      5      0
## straw-its2-D13-3      0      0      0      0      0      0      0      2      0
## straw-its2-D14-1      0      0      0      0      0      0      0     13      0
## straw-its2-D14-2      0      0      0      0      0      9      0      0      0
## straw-its2-D14-3      0      0      0     22      0      7      0      7      0
## straw-its2-D14-4      0      0      0     13      0      0      0     15      0
## straw-its2-D14-5      0      0     11      9      0      0      0      8      0
## straw-its2-D15-1      0      0      0      0      0      0      0      6      0
## straw-its2-D15-2      0      0      0      0      0      8      0      3    119
## straw-its2-D15-3      0      0     26     10      0      0      0      0      0
##                  Seq237 Seq238 Seq239 Seq240 Seq241 Seq242 Seq243 Seq244 Seq245
## straw-its2-D01-1      0      0      0      0      0    111      0      0     31
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0     51      0      0      0      0    110      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0     29
## straw-its2-D03-2      0     13      0    113      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      4
## straw-its2-D05-1      0      0     53      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      3
## straw-its2-D05-3      0      0      0      0      0      0      0      0      3
## straw-its2-D05-4    118      0      0      0      0      0      0      0     12
## straw-its2-D05-5      0      2      0      0      0      0      0      0     27
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0     15      0      0      0      0    110      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0     49      6      0      0      0      0      0      0
## straw-its2-D12-2      0      0     33      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0    113      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      3      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      1      0      0      0      0      0      0
## straw-its2-D14-3      0      0      1      0      0      0      0      0      0
## straw-its2-D14-4      0      0      1      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      1      0      0      0      0      0      0
##                  Seq246 Seq247 Seq248 Seq249 Seq250 Seq251 Seq252 Seq253 Seq254
## straw-its2-D01-1      0      0      0     12      0      0      0      0      0
## straw-its2-D01-2      0      0      0     49      0      0      0      0      0
## straw-its2-D01-3      6      0      0     44      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      1      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0    106      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0    109      0      0      0      0      0    102      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0     16
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      2
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0    108      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0     20
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      5      0      0      0      0      0      0      0     43
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      3      0      0      0      0      0      0      0      0
## straw-its2-D14-1     65      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0    104      0      0     20
## straw-its2-D14-4      1      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1     29      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0    103      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq255 Seq256 Seq257 Seq258 Seq259 Seq260 Seq261 Seq262 Seq263
## straw-its2-D01-1      0     56      0      0      0      0      0     72     49
## straw-its2-D01-2      0     24      0      0      0      0      0      1      4
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      9      0      0      0      0      0      7     19
## straw-its2-D03-2      0      0      0      0      0      0      0      2      0
## straw-its2-D03-3      0      4      0      0      0      0      0      4      1
## straw-its2-D05-1      0      1      0      0      0      0      0      0      1
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      3      0      0      0     95      0      4      2
## straw-its2-D05-4      0      1      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      3      2
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0     85      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      1      0      0      0      0      0      0      1
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      9      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1    101      0      0      0      0      0      0      0      8
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0     99      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      1      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      3
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      2
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0     98      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0     98      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq264 Seq265 Seq266 Seq267 Seq268 Seq269 Seq270 Seq271 Seq272
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0     87      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0     84      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2     91      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0     87      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      1
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0     17
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0     28
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0     85      0      0      0
## straw-its2-D14-2      0     90      0      0      0      0      0      0      6
## straw-its2-D14-3      0      0      0      0     87      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      7
## straw-its2-D14-5      0      0      0      0      0      0      0      0     21
## straw-its2-D15-1      0      0      0      0      0      0     85      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      4
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq273 Seq274 Seq275 Seq276 Seq277 Seq278 Seq279 Seq280 Seq281
## straw-its2-D01-1      0      0      0      2     79      0      0     76     13
## straw-its2-D01-2      0      0      0     51      0      0      0      0      0
## straw-its2-D01-3      0      0      0     26      0      0      0      0      0
## straw-its2-D03-1     40      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3     23      0      0      0      0     79      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0     13
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0     79      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      2      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0     10      0      0      0      0      0      0
## straw-its2-D10-2      0      0     12      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0     35      0      0      0      0      0      0
## straw-its2-D10-5      0      0      2      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      9
## straw-its2-D12-2      0      0      3      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1     19      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      6      0      0      0      0      0      0
## straw-its2-D13-3      0      0      3      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0     10
## straw-its2-D14-2      0      0      1      0      0      0      0      0     12
## straw-its2-D14-3      0      0      0      0      0      0      0      0     15
## straw-its2-D14-4      0     83      3      0      0      0      0      0      0
## straw-its2-D14-5      0      0      3      0      0      0      0      0      3
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      1      0      0      0      0      0      0
## straw-its2-D15-3      1      0      0      0      0      0      0      0      0
##                  Seq282 Seq283 Seq284 Seq285 Seq286 Seq287 Seq288 Seq289 Seq290
## straw-its2-D01-1     52      0      0      0      0      0      0      0      0
## straw-its2-D01-2      1      0      0      0      0      0      0      0      0
## straw-its2-D01-3      1      0      0      0      0      0      0      0      0
## straw-its2-D03-1     10      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      1      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      1      0      0      0      0      0      0      0      0
## straw-its2-D05-4      5     74      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0     74      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      6      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0     20      0      0      0     73      0
## straw-its2-D12-2      0      0      0     18      0      0      0      0      0
## straw-its2-D12-3      0      0      0      3      0      0      0      0     71
## straw-its2-D13-1      1      0      0      2      0      0      0      0      0
## straw-its2-D13-2      0      0      0      9      0      0      0      0      0
## straw-its2-D13-3      0      0      0      1      0      0      0      0      0
## straw-its2-D14-1      0      0      0      1      0      0      0      0      0
## straw-its2-D14-2      0      0      0      9     74      0      0      0      0
## straw-its2-D14-3      1      0      0      1      0      0      0      0      0
## straw-its2-D14-4      0      0      0      2      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0     74      0      0      0
## straw-its2-D15-1      1      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      2      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0     74      0      0
##                  Seq291 Seq292 Seq293 Seq294 Seq295 Seq296 Seq297 Seq298 Seq299
## straw-its2-D01-1      0      0      0      0     67      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0     69      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0     65      0      0      0
## straw-its2-D05-3      0      0     69      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0     64
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0     68      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0     65      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      2      0
## straw-its2-D10-3     70      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      7      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      7      0
## straw-its2-D13-3      0      0      0      0      0      0      0      3      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      7      0
## straw-its2-D14-3      0      0      0      0      0      0      0      2      0
## straw-its2-D14-4      0      0      0      0      0      0      0     11      0
## straw-its2-D14-5      0      0      0      0      0      0      0      7      0
## straw-its2-D15-1      0      0      0      0      0      0      0     16      0
## straw-its2-D15-2      0      0      0      0      0      0      0      1      0
## straw-its2-D15-3      0      0      0      0      0      0      0      2      0
##                  Seq300 Seq301 Seq302 Seq303 Seq304 Seq305 Seq306 Seq307 Seq308
## straw-its2-D01-1      0      0      0     48      0      0     52     24      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0     38      8      0      0      5      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      1      0      0      0      3     34
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0     19     20
## straw-its2-D05-4      0      0      0      2      0      0      3      0      0
## straw-its2-D05-5      0      0      0      3      0      0      0      0      6
## straw-its2-D07-1      0      0      0      0      0     61      0      2      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3     64      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      2      0
## straw-its2-D08-3      0      0      9      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      1      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0     16      0      0      0      0      2      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      3      0
## straw-its2-D13-1      0      0      0      0      0      0      0      3      0
## straw-its2-D13-2      0      0      0      0      0      0      0      1      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0     62      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0     64      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq309 Seq310 Seq311 Seq312 Seq313 Seq314 Seq315 Seq316 Seq317
## straw-its2-D01-1      0     33      0      0     38      2      0      0      0
## straw-its2-D01-2      0      0      0      0      6     42     43      0      0
## straw-its2-D01-3      0      0      0      0      0     14     15      0      0
## straw-its2-D03-1      0      2      5      0      2      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      3      0      0      0      0
## straw-its2-D05-1      4      1      3      0      5      0      0      0      0
## straw-its2-D05-2      0      4     19      0      1      0      0      0      0
## straw-its2-D05-3      0      2     11      0      0      0      0      0      0
## straw-its2-D05-4      0     12     18      0      0      0      0      0      0
## straw-its2-D05-5      0      1      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      8      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0     59      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0     58      0
## straw-its2-D08-2      5      0      0      0      0      0      0      0     13
## straw-its2-D08-3      0      0      1      0      0      0      0      0      0
## straw-its2-D10-1      0      0      1      0      0      0      0      0      3
## straw-its2-D10-2     10      0      1      0      0      0      0      0      5
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      2      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1     21      0      0      0      0      0      0      0      8
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      5      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      6
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      2      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      8
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      7      2      0      0      1      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0     11
## straw-its2-D15-3      0      0      0      0      0      0      0      0      4
##                  Seq318 Seq319 Seq320 Seq321 Seq322 Seq323 Seq324 Seq325 Seq326
## straw-its2-D01-1      0      0     56      0     54      0      0      0     52
## straw-its2-D01-2      0      0      0     55      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0     54      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2     58      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0     53      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0     54      0      0
## straw-its2-D14-3      0     58      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq327 Seq328 Seq329 Seq330 Seq331 Seq332 Seq333 Seq334 Seq335
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0     50      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0     51      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0     51      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0     51      0     50
## straw-its2-D07-3     52      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0     52      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0     52      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0     52      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq336 Seq337 Seq338 Seq339 Seq340 Seq341 Seq342 Seq343 Seq344
## straw-its2-D01-1      0     11      0      0      0     48      0      0      0
## straw-its2-D01-2      0     29      0      0      0      0      0      0     47
## straw-its2-D01-3      0      4      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      4     45      0      0      0      0      0      0
## straw-its2-D03-3      0      1      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      7      0      0      0      0      0
## straw-its2-D05-3      0      0      0     10      0      0      0      0      0
## straw-its2-D05-4      0      0      0      8      0      0      0      0      0
## straw-its2-D05-5      0      0      0     15      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0     48      0      0
## straw-its2-D07-3      0      0      0      0     49      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      1      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5     50      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      1      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0     48      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      5      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      4      2      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq345 Seq346 Seq347 Seq348 Seq349 Seq350 Seq351 Seq352 Seq353
## straw-its2-D01-1      0      0      0      0      0     45      3      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      3      0      0
## straw-its2-D03-1      0      0      0      0      0      0      2      0     44
## straw-its2-D03-2      0      0      0      0      0      0      1      0      0
## straw-its2-D03-3      1      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      2      0      0      0      0      0      0      0
## straw-its2-D05-2      2      2      0      0      0      0      0     45      0
## straw-its2-D05-3     14      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0     10      0      0      0      0      0      0      0
## straw-its2-D05-5     12      2      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0     46      0      0      0      0      0
## straw-its2-D08-1      0      3      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      1      0      0
## straw-its2-D08-3      0      1      0      0      0      0      0      0      0
## straw-its2-D10-1      0     16      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      3      0      0
## straw-its2-D10-3      0      4     47      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      2      0      0
## straw-its2-D10-5      0      1      0      0      0      0      0      0      0
## straw-its2-D12-1      3      0      0      0      0      0      5      0      0
## straw-its2-D12-2      0      0      0      0      0      0      3      0      0
## straw-its2-D12-3      1      4      0      0      0      0      0      0      0
## straw-its2-D13-1      0      1      0      0      0      0      3      0      0
## straw-its2-D13-2      0      1      0      0     46      0      0      0      0
## straw-its2-D13-3      1      0      0      0      0      0      6      0      0
## straw-its2-D14-1      0      0      0      0      0      0      7      0      0
## straw-its2-D14-2      0      0      0      0      0      0      3      0      0
## straw-its2-D14-3      2      0      0      0      0      0      1      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      1      0      0
## straw-its2-D15-1     11      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      1      0      0
##                  Seq354 Seq355 Seq356 Seq357 Seq358 Seq359 Seq360 Seq361 Seq362
## straw-its2-D01-1      0      0      0      0     37     19      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      2     11      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0     12      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3     44      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0     44      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0     42      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0     18     43      0      0      0      1      0
## straw-its2-D10-2      0      0      0      0      0      0      0      5      0
## straw-its2-D10-3      0      0      1      0      0      0      0      0      0
## straw-its2-D10-4      0      0      3      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      6      0      0      0      0     13      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      2      0      0      0      0      1      0
## straw-its2-D13-1      0      0      3      0      3      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      3      0
## straw-its2-D13-3      0      0      7      0      0      0      0      2      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0     12      0
## straw-its2-D14-3      0      0      2      0      0      0      0      2      0
## straw-its2-D14-4      0      0      1      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0     42
## straw-its2-D15-1      0      0      1      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      3      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq363 Seq364 Seq365 Seq366 Seq367 Seq368 Seq369 Seq370 Seq371
## straw-its2-D01-1      2     40      0      0      0     35      0      0      0
## straw-its2-D01-2     30      0      0      0      0      0      0      0      0
## straw-its2-D01-3      8      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      2      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      4      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0     40      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      1      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      2      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0     40      0     39      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      3      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      2      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0     39      0
## straw-its2-D15-1      0      0     30      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0     39
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq372 Seq373 Seq374 Seq375 Seq376 Seq377 Seq378 Seq379 Seq380
## straw-its2-D01-1      0      0      0      0      0      0     36      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      2      0      0      0      0      0      0
## straw-its2-D03-1      1      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0     37      0      0      0      0      0
## straw-its2-D03-3      1      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      3      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0     37      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0     36      0
## straw-its2-D08-1      6      0      0      0      0      0      0      0      0
## straw-its2-D08-2      3      0      0      0      0      0      0      0      0
## straw-its2-D08-3      3      0      0      0      0      0      0      0      0
## straw-its2-D10-1      9      0      1      0      0      0      0      0      0
## straw-its2-D10-2      1      0      2      0      0      0      0      0      0
## straw-its2-D10-3      5      0      4      0      0      0      0      0     35
## straw-its2-D10-4      0      0      2      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      3      0      3      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      2      0      0      0      0      0      0
## straw-its2-D13-1      0      0      3      0      0      0      0      0      0
## straw-its2-D13-2      0     38      0      0      0     37      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      3      0      0      0      0      0      0
## straw-its2-D14-4      3      0      4      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0     11      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq381 Seq382 Seq383 Seq384 Seq385 Seq386 Seq387 Seq388 Seq389
## straw-its2-D01-1      0      0     12      2      0      0      0      0      0
## straw-its2-D01-2      0      0      5     16     33      0      0      0      0
## straw-its2-D01-3      0      0      0     15      0      0      0      0      0
## straw-its2-D03-1      0      0      3      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0     18      0      0      0
## straw-its2-D05-3      0      0      1      0      0      6      0      0      0
## straw-its2-D05-4      0      0      2      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      1      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0     33      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0     34      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      1      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      2      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      1      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0     33      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      1      0      0      0      0      0      0
## straw-its2-D14-1      0      0      1      0      0      0      0      0      0
## straw-its2-D14-2      0      0      2      0      0      0      0      0      0
## straw-its2-D14-3     35      0      2      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0     33
## straw-its2-D15-1      0      0      0      0      0      6      0      0      0
## straw-its2-D15-2      0      0      1      0      0      1      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq390 Seq391 Seq392 Seq393 Seq394 Seq395 Seq396 Seq397 Seq398
## straw-its2-D01-1     32      2      0      0      0      0      0      0      0
## straw-its2-D01-2      0     23      0      0      0      0      0      0      0
## straw-its2-D01-3      0      5      0      0      0      0      0      1      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0     32      0      0      0      0      0      3
## straw-its2-D05-1      0      0      0      0      0      0      0      0      1
## straw-its2-D05-2      0      0      0     32      0      0      0      0      2
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0     20
## straw-its2-D05-5      0      0      0      0      0      0      0      0      4
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      9      0      0      0      0
## straw-its2-D10-2      0      0      0      0      8      0      0      0      0
## straw-its2-D10-3      0      0      0      0      1      0      0      0      0
## straw-its2-D10-4      0      0      0      0      7      0      0      0      0
## straw-its2-D10-5      0      0      0      0      1      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      9     20      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      3      0
## straw-its2-D13-2      0      0      0      0      0      5      8      0      0
## straw-its2-D13-3      0      0      0      0      0      0      1      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      2      0
## straw-its2-D14-2      0      0      0      0      0      5     11      0      0
## straw-its2-D14-3      0      0      0      0      3      0      0      2      0
## straw-its2-D14-4      0      0      0      0      0      0      0      1      0
## straw-its2-D14-5      0      2      0      0      1      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      2      0      0
## straw-its2-D15-2      0      0      0      0      2     11      0      1      0
## straw-its2-D15-3      0      0      0      0      0     11      0      0      0
##                  Seq399 Seq400 Seq401 Seq402 Seq403 Seq404 Seq405 Seq406 Seq407
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1     30      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0     29      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0     29
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0     30     30      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0     30     30      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0     30      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0     30      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq408 Seq409 Seq410 Seq411 Seq412 Seq413 Seq414 Seq415 Seq416
## straw-its2-D01-1      8      0      0      0      0     21      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      2      0      0      0
## straw-its2-D03-2      0      3      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0     28      0      0      0      0      0      0
## straw-its2-D05-1      0      2      0      0      0      0      0      0      0
## straw-its2-D05-2      0     10      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0     27      0      0
## straw-its2-D05-4      0     12      0      0      0      2      0      0      0
## straw-its2-D05-5      1      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      1      0      0      0      0      0      0     27      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0     27
## straw-its2-D08-1      5      0      0      0      0      0      0      0      0
## straw-its2-D08-2      4      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      1      0      0      0      0      0      0      0
## straw-its2-D10-2      1      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      3      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0     28      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      1      0      0      0
## straw-its2-D13-3      5      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      1      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0     28      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq417 Seq418 Seq419 Seq420 Seq421 Seq422 Seq423 Seq424 Seq425
## straw-its2-D01-1      0      0      0      0      0     22      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0     25     21      0
## straw-its2-D01-3      0      0      0      0      0      0      0      4      0
## straw-its2-D03-1      0      0      0      0      0      3      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      3
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3     27      0      0      0     26      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0     10
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0     11
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0     16      6     27      0      0      0      0      0
## straw-its2-D12-2      0      1      0      0      0      0      0      0      1
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      2      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      3      0      0      0      0      0      0
## straw-its2-D14-2      0      3      3      0      0      0      0      0      0
## straw-its2-D14-3      0      6      0      0      0      0      0      0      0
## straw-its2-D14-4      0      1      5      0      0      0      0      0      0
## straw-its2-D14-5      0      0      8      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq426 Seq427 Seq428 Seq429 Seq430 Seq431 Seq432 Seq433 Seq434
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      1      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      2      0      0      0
## straw-its2-D03-3      0      0      0      0      0      7      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      9      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0     23      0      0
## straw-its2-D05-4      0      0      0      0      1      0      0     23      0
## straw-its2-D05-5      0      0      0      0      0      5      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3     25      0      0      0      0      0      0      0     23
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      3      0      0      0      0
## straw-its2-D08-3      0      0      0      0     11      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      1      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0     25      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      3      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      1      0      0      0      0
## straw-its2-D13-2      0      0      0     17      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      1      0      0      0      0
## straw-its2-D14-2      0      0      0      1      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      1      0      0      0      0
## straw-its2-D14-5      0      0      0      3      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0     25      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      3      0      0      0      0
##                  Seq435 Seq436 Seq437 Seq438 Seq439 Seq440 Seq441 Seq442 Seq443
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0     22      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      1      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      1      1      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      9      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      1      0      0
## straw-its2-D05-5      0      0      0      0      0      1      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3     23      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      8      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      1      0      0      0      0      7      0      0
## straw-its2-D10-2      0      9      0      0      0      2      3      6      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0     23      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      8
## straw-its2-D12-2      0      0      0      0      0      2      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      5
## straw-its2-D13-1      0      9      0      0      0      1      0      2      0
## straw-its2-D13-2      0      0      0      0      0      2      0      6      2
## straw-its2-D13-3      0      0      0      0      0      0      0      0      1
## straw-its2-D14-1      0      0      0      0      0      0      0      1      0
## straw-its2-D14-2      0      0      0      0      0      3      0      4      0
## straw-its2-D14-3      0      0      0      0      0      0      0      1      0
## straw-its2-D14-4      0      0      0     23      0      0      0      0      0
## straw-its2-D14-5      0      4      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      2      6
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      2      0      0
##                  Seq444 Seq445 Seq446 Seq447 Seq448 Seq449 Seq450 Seq451 Seq452
## straw-its2-D01-1      0      0     21     15     15     21      1      0      0
## straw-its2-D01-2      0      0      0      0      1      0      0     21      0
## straw-its2-D01-3      0      0      0      0      0      0      2      0      4
## straw-its2-D03-1      0      0      0      2      3      0      2      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      4      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      1      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      3
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      3
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      1      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      4      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      3      0      0
## straw-its2-D13-1      0      0      0      0      0      0      3      0     11
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      3      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1     22     22      0      0      0      0      1      0      0
## straw-its2-D15-2      0      0      0      0      2      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq453 Seq454 Seq455 Seq456 Seq457 Seq458 Seq459 Seq460 Seq461
## straw-its2-D01-1      0      0      0      1      0      0      0      0     19
## straw-its2-D01-2      0      0      0     11      0      0      0      0      0
## straw-its2-D01-3      0      0      0      6      1      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      6      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      2      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2     21      0      0      0      1      0      0      0      0
## straw-its2-D05-3      0      7      0      0      0      6      0      0      0
## straw-its2-D05-4      0      0      0      0      0      2      0      0      0
## straw-its2-D05-5      0      0      0      0      0      4      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0     20      0      0
## straw-its2-D07-3      0      0     21      0      0      0      0      0      0
## straw-its2-D08-1      0      5      0      0      5      0      0      0      0
## straw-its2-D08-2      0      0      0      0      4      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      1      0      0      0      0
## straw-its2-D10-2      0      5      0      0      1      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      1      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      4      0      0      0      0
## straw-its2-D14-1      0      4      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      1      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      1      0      0      0      0
## straw-its2-D15-2      0      0      0      2      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0     20      0
##                  Seq462 Seq463 Seq464 Seq465 Seq466 Seq467 Seq468 Seq469 Seq470
## straw-its2-D01-1      0      0      0      0      0     18      0      0      0
## straw-its2-D01-2     16      0      0      0      0      0      0      0      0
## straw-its2-D01-3      3      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      1      1      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      6
## straw-its2-D05-2      0      0      0      0      0      0      0      3      0
## straw-its2-D05-3      0      0      0      0      0      0      0      7      0
## straw-its2-D05-4      0      0      0      0      0      0      0      4     10
## straw-its2-D05-5      0      0      0      0      0      0      0      0      2
## straw-its2-D07-1      0     19      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0     19      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      7      0      0      0      2      0
## straw-its2-D10-2      0      0      0      0      0      0      0      1      0
## straw-its2-D10-3      0      0      0      2      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      3      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0     19      0      3      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      8      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      2      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      6      0      0
## straw-its2-D14-2      0      0      0      0      0      0      2      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      3      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq471 Seq472 Seq473 Seq474 Seq475 Seq476 Seq477 Seq478 Seq479
## straw-its2-D01-1      0      0      0     17     17     11      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0     17     17     10
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      1      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      4      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      4      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      2      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0     18      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      7      0      0      2      0      0      0
## straw-its2-D10-2      1      0      3      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      3      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      1      0      0      0
## straw-its2-D13-1      1      0      0      0      0      0      0      0      0
## straw-its2-D13-2      1      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      5      0      0      0      0      0      0
## straw-its2-D15-1      6      0      0      0      0      0      0      0      7
## straw-its2-D15-2      1      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq480 Seq481 Seq482 Seq483 Seq484 Seq485 Seq486 Seq487 Seq488
## straw-its2-D01-1      0      0      0      0      0      0      0      0     16
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      1      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      4      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      2      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0     17      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0     17      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      6      2      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      3      0      0      0      0      0      0      0
## straw-its2-D10-2      1      0      0      0      5      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0     17      0      0      0
## straw-its2-D10-4      0      4      0      0      0      0     17     17      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      4      0      0      0      0
## straw-its2-D12-2      2      0      0      0      4      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      3      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      5      0      0      0      1      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      1      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      2      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      1      0      0      0      0      0      0      0      0
##                  Seq489 Seq490 Seq491 Seq492 Seq493 Seq494 Seq495 Seq496 Seq497
## straw-its2-D01-1     16     16     16      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0     16      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      4      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      5     16      0      0      0
## straw-its2-D05-3      0      0      0      0      5      0     11     16      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      5      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0     16
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      1      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      1      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq498 Seq499 Seq500 Seq501 Seq502 Seq503 Seq504 Seq505 Seq506
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      5      0      0      0      0      0
## straw-its2-D01-3      0      0      0     10      2      0      0      0      0
## straw-its2-D03-1      0      0      0      0      1      2      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      1      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0     15      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0     15      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0     15
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      6      0      0      0
## straw-its2-D08-2      0      0      0      0      1      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      6      0      0      0      0      4      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      2      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      3      0      0      0      2      0      0      0      0
## straw-its2-D14-2      2      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0     16      0      0      0      0      0      0      0
## straw-its2-D15-2      5      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0     16      0      9      0      0      0      0
##                  Seq507 Seq508 Seq509 Seq510 Seq511 Seq512 Seq513 Seq514 Seq515
## straw-its2-D01-1      0      0      0      0      0     14      9     14     14
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      5      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2     15      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0     15      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      4      5      0      0      0      0      0
## straw-its2-D10-2      0      0      8      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      1      3      4      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      1      6      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      3      0      0      0      0
## straw-its2-D12-3      0      0      1      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      8      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      1      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq516 Seq517 Seq518 Seq519 Seq520 Seq521 Seq522 Seq523 Seq524
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2     14      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0     14      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      1      0      0      0      0      0      0
## straw-its2-D05-2      0      0      3      1      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      3      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      3      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      3     14      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0     14      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      7      0      0
## straw-its2-D08-2      0      0      0      1      0      0      0      3      1
## straw-its2-D08-3      0      0      0      1      0      0      0      0      0
## straw-its2-D10-1      0      0      2      0      0      0      0      2      0
## straw-its2-D10-2      0      0      1      2      0      0      0      0      0
## straw-its2-D10-3      0      0      2      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      3      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      1      0      0      0      1      0      5
## straw-its2-D12-2      0      0      0      0      0      0      0      0      3
## straw-its2-D12-3      0      0      1      0      0      0      1      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      1      4
## straw-its2-D13-3      0      0      0      0      0      0      0      1      0
## straw-its2-D14-1      0      0      0      0      0      0      5      0      1
## straw-its2-D14-2      0      0      0      0      0      0      0      1      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      1      0      0      0      0      0
## straw-its2-D14-5      0      0      0      2      0      0      0      3      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq525 Seq526 Seq527 Seq528 Seq529 Seq530 Seq531 Seq532 Seq533
## straw-its2-D01-1      0      0      0      0      0     13      3      0      0
## straw-its2-D01-2      0      0      0      0      0      0      8      0      0
## straw-its2-D01-3      0      0      0      0      0      0      2      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      3      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0     13
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      3      0
## straw-its2-D05-4      0      0      0      0      0      0      0      7      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      4      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4     10      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      4      3      0      0      0      0      0      0
## straw-its2-D12-2      0      1      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      2      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0     14      0      0      0      0      0
## straw-its2-D14-1      0      2      2      0      0      0      0      0      0
## straw-its2-D14-2      0      5      5      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      1      0     14      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      1      0      0      0      0      0      0
## straw-its2-D15-3      0      0      2      0      0      0      0      0      0
##                  Seq534 Seq535 Seq536 Seq537 Seq538 Seq539 Seq540 Seq541 Seq542
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2     13      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0     13      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0     13     13     13      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0     13      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      3      0      0
## straw-its2-D10-2      0      0      0      0      0      0      6      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      3      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      2      1      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      4      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      2      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      5      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0     13
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq543 Seq544 Seq545 Seq546 Seq547 Seq548 Seq549 Seq550 Seq551
## straw-its2-D01-1     12     12     12      5      7      3     12      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0     12     12
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      2      4      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      1      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      3      4      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      2      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      2      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      3      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq552 Seq553 Seq554 Seq555 Seq556 Seq557 Seq558 Seq559 Seq560
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2     12      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      6      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      8      0      0      0      0      0      0
## straw-its2-D03-3      0      1      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      4      4      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0     12     12      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0     12      0      0      0
## straw-its2-D05-5      0      1      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      2     12      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0     12
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      1      0      0
## straw-its2-D10-4      0      0      0      0      0      0      1      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      1      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      3      0      0
## straw-its2-D14-3      0      0      0      0      0      0      2      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      1      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      1      0      0
##                  Seq561 Seq562 Seq563 Seq564 Seq565 Seq566 Seq567 Seq568 Seq569
## straw-its2-D01-1      0      0      0     11     11     11      4      4      0
## straw-its2-D01-2      0      0      0      0      0      0      2      0      8
## straw-its2-D01-3      0      0      0      0      0      0      0      0      3
## straw-its2-D03-1      0      0      0      0      0      0      0      7      0
## straw-its2-D03-2      0      0      0      0      0      0      3      0      0
## straw-its2-D03-3      0      0      0      0      0      0      2      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      4      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      2      0      0      0      0      0      0      0
## straw-its2-D10-3      4      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      1      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      2      9      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      1      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      1      3      0      0      0      0      0      0
## straw-its2-D13-3      0      0      1      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      1      0      0      0      0      0      0
## straw-its2-D14-4      1      0      6      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq570 Seq571 Seq572 Seq573 Seq574 Seq575 Seq576 Seq577 Seq578
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      8     11      3      0      0      0      0      0      0
## straw-its2-D03-1      3      0      0      2      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      1      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      4      2      0      0      0      0      0
## straw-its2-D05-2      0      0      2      0      0      8      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      3      0      0      0
## straw-its2-D05-5      0      0      1      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0     11      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      3      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      1      0      0      0      2      1
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      1      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      4      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      1      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      3      2
## straw-its2-D14-1      0      0      0      0      0      0      0      5      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      4
## straw-its2-D14-3      0      0      0      2      0      0      0      1      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      2
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      1      0      5      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      2
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq579 Seq580 Seq581 Seq582 Seq583 Seq584 Seq585 Seq586 Seq587
## straw-its2-D01-1      0      0      0      0     10     10     10      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0     10     10
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      4      6     11      0      0      0      0      0      0
## straw-its2-D12-2      3      0      0      0      0      0      0      0      0
## straw-its2-D12-3      3      2      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      1      0      0      0      0      0      0      0
## straw-its2-D14-5      1      2      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0     11      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq588 Seq589 Seq590 Seq591 Seq592 Seq593 Seq594 Seq595 Seq596
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1     10      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      1      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      2      2      0      0      0      0      0      0
## straw-its2-D05-3      0      4      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      3      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0     10     10      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0     10      0      0      0
## straw-its2-D08-1      0      0      1      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      6      0      0      0      2      0      0
## straw-its2-D10-2      0      0      1      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0     10      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      3
## straw-its2-D12-2      0      0      0      0      0      0      0      0      1
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      4      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      3
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      2
## straw-its2-D14-5      0      0      0      0      0      0      0      0      1
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      4      0      0
##                  Seq597 Seq598 Seq599 Seq600 Seq601 Seq602 Seq603 Seq604 Seq605
## straw-its2-D01-1      0      9      9      1      0      0      0      0      0
## straw-its2-D01-2      0      0      0      2      6      9      9      9      0
## straw-its2-D01-3      0      0      0      3      3      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      1
## straw-its2-D03-3      0      0      0      1      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      2
## straw-its2-D05-3      0      0      0      2      0      0      0      0      2
## straw-its2-D05-4      0      0      0      0      0      0      0      0      2
## straw-its2-D05-5      0      0      0      0      0      0      0      0      2
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1     10      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq606 Seq607 Seq608 Seq609 Seq610 Seq611 Seq612 Seq613 Seq614
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      5      5      3      0      0      0      0      0      0
## straw-its2-D05-3      0      3      0      0      0      0      0      0      0
## straw-its2-D05-4      0      1      4      0      0      0      0      0      0
## straw-its2-D05-5      0      0      2      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      3      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      9      1      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      9      9      2
## straw-its2-D13-2      0      0      0      5      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      1
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      2      0      0      4
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      4      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      3      0      0      2
## straw-its2-D15-1      0      0      0      0      0      3      0      0      0
## straw-its2-D15-2      0      0      0      1      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq615 Seq616 Seq617 Seq618 Seq619 Seq620 Seq621 Seq622 Seq623
## straw-its2-D01-1      0      8      8      8      8      6      8      8      8
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      2      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      9      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq624 Seq625 Seq626 Seq627 Seq628 Seq629 Seq630 Seq631 Seq632
## straw-its2-D01-1      8      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      8      8      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      3      0      0      0      0      0
## straw-its2-D03-2      0      0      0      5      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      8      8      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      8      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      8      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      8
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq633 Seq634 Seq635 Seq636 Seq637 Seq638 Seq639 Seq640 Seq641
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      4      1      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      6      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      4      0      0      0      0      0
## straw-its2-D10-2      0      2      0      2      4      8      8      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      2      0      0      0      4      0      0      8      5
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      2      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      1      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      2      5      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      3
## straw-its2-D15-3      0      0      0      1      0      0      0      0      0
##                  Seq642 Seq643 Seq644 Seq645 Seq646 Seq647 Seq648 Seq649 Seq650
## straw-its2-D01-1      0      0      0      0      7      7      7      7      7
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      8      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      8      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      3      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      2      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      3      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      8      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq651 Seq652 Seq653 Seq654 Seq655 Seq656 Seq657 Seq658 Seq659
## straw-its2-D01-1      7      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      7      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      2      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      3      7      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      7      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      3      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      4      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      4      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      7      7
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      5      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq660 Seq661 Seq662 Seq663 Seq664 Seq665 Seq666 Seq667 Seq668
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      7      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      4      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      5      7      7      2      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      2      0      0      0      4      2      0
## straw-its2-D13-2      0      0      0      0      0      5      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      7
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      3      0      0      0      0      3      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      5      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq669 Seq670 Seq671 Seq672 Seq673 Seq674 Seq675 Seq676 Seq677
## straw-its2-D01-1      0      0      0      0      0      0      6      6      6
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      7      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      7      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      7      7      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      7      7      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq678 Seq679 Seq680 Seq681 Seq682 Seq683 Seq684 Seq685 Seq686
## straw-its2-D01-1      2      6      6      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      6      6      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      3      0      0      0
## straw-its2-D03-1      4      0      0      0      0      0      6      2      6
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      1      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      2      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      1      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      3      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq687 Seq688 Seq689 Seq690 Seq691 Seq692 Seq693 Seq694 Seq695
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      6      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      6      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      2      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      6      6      3      3      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      6      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      4      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      6
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      3      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      3      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq696 Seq697 Seq698 Seq699 Seq700 Seq701 Seq702 Seq703 Seq704
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      4      0      0      0      0      0      0      0      0
## straw-its2-D10-2      2      6      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      6      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      6      6      6      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      2      6      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      3
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      4      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      3
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq705 Seq706 Seq707 Seq708 Seq709 Seq710 Seq711 Seq712 Seq713
## straw-its2-D01-1      0      0      0      0      0      5      5      5      5
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      6      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      6      6      6      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      6      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq714 Seq715 Seq716 Seq717 Seq718 Seq719 Seq720 Seq721 Seq722
## straw-its2-D01-1      5      5      5      5      5      5      5      2      5
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      3      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq723 Seq724 Seq725 Seq726 Seq727 Seq728 Seq729 Seq730 Seq731
## straw-its2-D01-1      5      5      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      5      5      5      5      5      2      0
## straw-its2-D01-3      0      0      0      0      0      0      0      3      5
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq732 Seq733 Seq734 Seq735 Seq736 Seq737 Seq738 Seq739 Seq740
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      5      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      5      5      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      5      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      5      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      5      5      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      5      5
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq741 Seq742 Seq743 Seq744 Seq745 Seq746 Seq747 Seq748 Seq749
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      5      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      5      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      5      5      5      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      5      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      5      5      5
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq750 Seq751 Seq752 Seq753 Seq754 Seq755 Seq756 Seq757 Seq758
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      2      0      0      0      0      0      0      0      0
## straw-its2-D10-5      1      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      5      3      2      0      0      0      0      0
## straw-its2-D12-2      2      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      5      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      5      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      3      0      0      5      5      0
## straw-its2-D14-3      0      0      2      0      0      0      0      0      5
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq759 Seq760 Seq761 Seq762 Seq763 Seq764 Seq765 Seq766 Seq767
## straw-its2-D01-1      0      0      4      4      4      4      4      4      4
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      5      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      5      0      0      0      0      0      0      0
##                  Seq768 Seq769 Seq770 Seq771 Seq772 Seq773 Seq774 Seq775 Seq776
## straw-its2-D01-1      4      4      4      4      4      4      4      4      4
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq777 Seq778 Seq779 Seq780 Seq781 Seq782 Seq783 Seq784 Seq785
## straw-its2-D01-1      4      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      4      4      4      4      4      4      4      4
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq786 Seq787 Seq788 Seq789 Seq790 Seq791 Seq792 Seq793 Seq794
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      4      4      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      4      4      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      4      4      4      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      4      4
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq795 Seq796 Seq797 Seq798 Seq799 Seq800 Seq801 Seq802 Seq803
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      4      4      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      4      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      4      4      4      4      2      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      4
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      2      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq804 Seq805 Seq806 Seq807 Seq808 Seq809 Seq810 Seq811 Seq812
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      4      4      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      4      4      4      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      4      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      4      4      4
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq813 Seq814 Seq815 Seq816 Seq817 Seq818 Seq819 Seq820 Seq821
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      4      4      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      4      4      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      4      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      4      4      4      4
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq822 Seq823 Seq824 Seq825 Seq826 Seq827 Seq828 Seq829 Seq830
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      2      0      0      0      0      0      0      0      0
## straw-its2-D10-2      2      4      4      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      4      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      4      4      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      4      4      4
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq831 Seq832 Seq833 Seq834 Seq835 Seq836 Seq837 Seq838 Seq839
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      4      4      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      2      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      4      4      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      4      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      4      4      4
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      2      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq840 Seq841 Seq842 Seq843 Seq844 Seq845 Seq846 Seq847 Seq848
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      4      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      4      4      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      4      4      4      4      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      4      4
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq849 Seq850 Seq851 Seq852 Seq853 Seq854 Seq855 Seq856 Seq857
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      4      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      2      4      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      4      4      4      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      4      4      4
## straw-its2-D15-2      0      2      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq858 Seq859 Seq860 Seq861 Seq862 Seq863 Seq864 Seq865 Seq866
## straw-its2-D01-1      0      0      0      3      3      3      3      3      3
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      4      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      4      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      4      0      0      0      0      0      0
##                  Seq867 Seq868 Seq869 Seq870 Seq871 Seq872 Seq873 Seq874 Seq875
## straw-its2-D01-1      3      3      3      3      3      3      3      3      3
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq876 Seq877 Seq878 Seq879 Seq880 Seq881 Seq882 Seq883 Seq884
## straw-its2-D01-1      3      3      3      3      3      3      3      3      3
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq885 Seq886 Seq887 Seq888 Seq889 Seq890 Seq891 Seq892 Seq893
## straw-its2-D01-1      3      3      3      3      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      3      3      3      3      3
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq894 Seq895 Seq896 Seq897 Seq898 Seq899 Seq900 Seq901 Seq902
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      3      3      3      3      3      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      3      3      3      3
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq903 Seq904 Seq905 Seq906 Seq907 Seq908 Seq909 Seq910 Seq911
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      3      3      3      3      3      3      3      3      3
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq912 Seq913 Seq914 Seq915 Seq916 Seq917 Seq918 Seq919 Seq920
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      3      3      3      3      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      3      3      3      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      3      3
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq921 Seq922 Seq923 Seq924 Seq925 Seq926 Seq927 Seq928 Seq929
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      3      3      3      3      3      3      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      3      3      3
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq930 Seq931 Seq932 Seq933 Seq934 Seq935 Seq936 Seq937 Seq938
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      3      3      3      3      3      3      3      3      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      3
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq939 Seq940 Seq941 Seq942 Seq943 Seq944 Seq945 Seq946 Seq947
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      3      3      3      3      3      3      3      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      3      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      3
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq948 Seq949 Seq950 Seq951 Seq952 Seq953 Seq954 Seq955 Seq956
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      3      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      3      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      3      3      3      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      3      3      3      3
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq957 Seq958 Seq959 Seq960 Seq961 Seq962 Seq963 Seq964 Seq965
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      3      3      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      3      3      3      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      3      3      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      3      3
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq966 Seq967 Seq968 Seq969 Seq970 Seq971 Seq972 Seq973 Seq974
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      3      3      3      3      3      3      3      3      3
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq975 Seq976 Seq977 Seq978 Seq979 Seq980 Seq981 Seq982 Seq983
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      3      3      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      3      3      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      3      3      3      3      3
## straw-its2-D13-1      0      0      0      0      0      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      0      0      0      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      0
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq984 Seq985 Seq986 Seq987 Seq988 Seq989 Seq990 Seq991 Seq992
## straw-its2-D01-1      0      0      0      0      0      0      0      0      0
## straw-its2-D01-2      0      0      0      0      0      0      0      0      0
## straw-its2-D01-3      0      0      0      0      0      0      0      0      0
## straw-its2-D03-1      0      0      0      0      0      0      0      0      0
## straw-its2-D03-2      0      0      0      0      0      0      0      0      0
## straw-its2-D03-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-1      0      0      0      0      0      0      0      0      0
## straw-its2-D05-2      0      0      0      0      0      0      0      0      0
## straw-its2-D05-3      0      0      0      0      0      0      0      0      0
## straw-its2-D05-4      0      0      0      0      0      0      0      0      0
## straw-its2-D05-5      0      0      0      0      0      0      0      0      0
## straw-its2-D07-1      0      0      0      0      0      0      0      0      0
## straw-its2-D07-2      0      0      0      0      0      0      0      0      0
## straw-its2-D07-3      0      0      0      0      0      0      0      0      0
## straw-its2-D08-1      0      0      0      0      0      0      0      0      0
## straw-its2-D08-2      0      0      0      0      0      0      0      0      0
## straw-its2-D08-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-1      0      0      0      0      0      0      0      0      0
## straw-its2-D10-2      0      0      0      0      0      0      0      0      0
## straw-its2-D10-3      0      0      0      0      0      0      0      0      0
## straw-its2-D10-4      0      0      0      0      0      0      0      0      0
## straw-its2-D10-5      0      0      0      0      0      0      0      0      0
## straw-its2-D12-1      0      0      0      0      0      0      0      0      0
## straw-its2-D12-2      0      0      0      0      0      0      0      0      0
## straw-its2-D12-3      0      0      0      0      0      0      0      0      0
## straw-its2-D13-1      3      3      3      3      3      0      0      0      0
## straw-its2-D13-2      0      0      0      0      0      3      3      3      0
## straw-its2-D13-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-1      0      0      0      0      0      0      0      0      3
## straw-its2-D14-2      0      0      0      0      0      0      0      0      0
## straw-its2-D14-3      0      0      0      0      0      0      0      0      0
## straw-its2-D14-4      0      0      0      0      0      0      0      0      0
## straw-its2-D14-5      0      0      0      0      0      0      0      0      0
## straw-its2-D15-1      0      0      0      0      0      0      0      0      0
## straw-its2-D15-2      0      0      0      0      0      0      0      0      0
## straw-its2-D15-3      0      0      0      0      0      0      0      0      0
##                  Seq993 Seq994 Seq995 Seq996 Seq997 Seq998 Seq999 Seq1000
## straw-its2-D01-1      0      0      0      0      0      0      0       0
## straw-its2-D01-2      0      0      0      0      0      0      0       0
## straw-its2-D01-3      0      0      0      0      0      0      0       0
## straw-its2-D03-1      0      0      0      0      0      0      0       0
## straw-its2-D03-2      0      0      0      0      0      0      0       0
## straw-its2-D03-3      0      0      0      0      0      0      0       0
## straw-its2-D05-1      0      0      0      0      0      0      0       0
## straw-its2-D05-2      0      0      0      0      0      0      0       0
## straw-its2-D05-3      0      0      0      0      0      0      0       0
## straw-its2-D05-4      0      0      0      0      0      0      0       0
## straw-its2-D05-5      0      0      0      0      0      0      0       0
## straw-its2-D07-1      0      0      0      0      0      0      0       0
## straw-its2-D07-2      0      0      0      0      0      0      0       0
## straw-its2-D07-3      0      0      0      0      0      0      0       0
## straw-its2-D08-1      0      0      0      0      0      0      0       0
## straw-its2-D08-2      0      0      0      0      0      0      0       0
## straw-its2-D08-3      0      0      0      0      0      0      0       0
## straw-its2-D10-1      0      0      0      0      0      0      0       0
## straw-its2-D10-2      0      0      0      0      0      0      0       0
## straw-its2-D10-3      0      0      0      0      0      0      0       0
## straw-its2-D10-4      0      0      0      0      0      0      0       0
## straw-its2-D10-5      0      0      0      0      0      0      0       0
## straw-its2-D12-1      0      0      0      0      0      0      0       0
## straw-its2-D12-2      0      0      0      0      0      0      0       0
## straw-its2-D12-3      0      0      0      0      0      0      0       0
## straw-its2-D13-1      0      0      0      0      0      0      0       0
## straw-its2-D13-2      0      0      0      0      0      0      0       0
## straw-its2-D13-3      0      0      0      0      0      0      0       0
## straw-its2-D14-1      3      3      3      3      0      0      0       0
## straw-its2-D14-2      0      0      0      0      3      3      3       3
## straw-its2-D14-3      0      0      0      0      0      0      0       0
## straw-its2-D14-4      0      0      0      0      0      0      0       0
## straw-its2-D14-5      0      0      0      0      0      0      0       0
## straw-its2-D15-1      0      0      0      0      0      0      0       0
## straw-its2-D15-2      0      0      0      0      0      0      0       0
## straw-its2-D15-3      0      0      0      0      0      0      0       0
##                  Seq1001 Seq1002 Seq1003 Seq1004 Seq1005 Seq1006 Seq1007
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       3       0       0       0       0       0       0
## straw-its2-D14-3       0       3       3       3       3       0       0
## straw-its2-D14-4       0       0       0       0       0       3       0
## straw-its2-D14-5       0       0       0       0       0       0       3
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1008 Seq1009 Seq1010 Seq1011 Seq1012 Seq1013 Seq1014
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       3       3       3       0       0       0       0
## straw-its2-D15-1       0       0       0       3       3       3       3
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1015 Seq1016 Seq1017 Seq1018 Seq1019 Seq1020 Seq1021
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       3       3       3       3       3       3       0
## straw-its2-D15-2       0       0       0       0       0       0       3
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1022 Seq1023 Seq1024 Seq1025 Seq1026 Seq1027 Seq1028
## straw-its2-D01-1       0       0       0       0       2       2       2
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       3       0       0       0       0       0       0
## straw-its2-D15-3       0       3       3       3       0       0       0
##                  Seq1029 Seq1030 Seq1031 Seq1032 Seq1033 Seq1034 Seq1035
## straw-its2-D01-1       2       2       2       2       2       2       2
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1036 Seq1037 Seq1038 Seq1039 Seq1040 Seq1041 Seq1042
## straw-its2-D01-1       2       2       2       2       2       2       2
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1043 Seq1044 Seq1045 Seq1046 Seq1047 Seq1048 Seq1049
## straw-its2-D01-1       2       2       2       2       2       2       2
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1050 Seq1051 Seq1052 Seq1053 Seq1054 Seq1055 Seq1056
## straw-its2-D01-1       2       2       2       2       2       2       2
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1057 Seq1058 Seq1059 Seq1060 Seq1061 Seq1062 Seq1063
## straw-its2-D01-1       2       2       2       2       2       2       2
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1064 Seq1065 Seq1066 Seq1067 Seq1068 Seq1069 Seq1070
## straw-its2-D01-1       2       0       0       0       0       0       0
## straw-its2-D01-2       0       2       2       2       2       2       2
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1071 Seq1072 Seq1073 Seq1074 Seq1075 Seq1076 Seq1077
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       2       2       2       2       2       2       2
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1078 Seq1079 Seq1080 Seq1081 Seq1082 Seq1083 Seq1084
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       2       2       2       2       2       2       0
## straw-its2-D01-3       0       0       0       0       0       0       2
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1085 Seq1086 Seq1087 Seq1088 Seq1089 Seq1090 Seq1091
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       2       2       2       0       0       0       0
## straw-its2-D03-1       0       0       0       2       2       2       2
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1092 Seq1093 Seq1094 Seq1095 Seq1096 Seq1097 Seq1098
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       2       2       2       2       2       2       2
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1099 Seq1100 Seq1101 Seq1102 Seq1103 Seq1104 Seq1105
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       2       2       2       2       0       0       0
## straw-its2-D03-2       0       0       0       0       2       2       2
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1106 Seq1107 Seq1108 Seq1109 Seq1110 Seq1111 Seq1112
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       2       0       0       0       0       0       0
## straw-its2-D03-3       0       2       2       2       0       0       0
## straw-its2-D05-1       0       0       0       0       2       2       2
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1113 Seq1114 Seq1115 Seq1116 Seq1117 Seq1118 Seq1119
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       2       2       0       0       0       0       0
## straw-its2-D05-2       0       0       2       2       2       2       2
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1120 Seq1121 Seq1122 Seq1123 Seq1124 Seq1125 Seq1126
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       2       2       2       2       2       2       2
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1127 Seq1128 Seq1129 Seq1130 Seq1131 Seq1132 Seq1133
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       2       2       2       0       0       0       0
## straw-its2-D05-3       0       0       0       2       2       2       2
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1134 Seq1135 Seq1136 Seq1137 Seq1138 Seq1139 Seq1140
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       2       2       2       0       0       0       0
## straw-its2-D05-4       0       0       0       2       2       2       2
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1141 Seq1142 Seq1143 Seq1144 Seq1145 Seq1146 Seq1147
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       2       2       2       2       2       2       0
## straw-its2-D05-5       0       0       0       0       0       0       2
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1148 Seq1149 Seq1150 Seq1151 Seq1152 Seq1153 Seq1154
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       2       0       0       0       0       0       0
## straw-its2-D07-1       0       2       0       0       0       0       0
## straw-its2-D07-2       0       0       2       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       2       2       0       0
## straw-its2-D08-2       0       0       0       0       0       2       2
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1155 Seq1156 Seq1157 Seq1158 Seq1159 Seq1160 Seq1161
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       2       2       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       2       2       2       2       2
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1162 Seq1163 Seq1164 Seq1165 Seq1166 Seq1167 Seq1168
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       2       2       0       0       0       0       0
## straw-its2-D10-2       0       0       2       2       2       2       2
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1169 Seq1170 Seq1171 Seq1172 Seq1173 Seq1174 Seq1175
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       2       2       2       2       2       2       2
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1176 Seq1177 Seq1178 Seq1179 Seq1180 Seq1181 Seq1182
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       2       0       0       0       0       0       0
## straw-its2-D10-3       0       2       2       0       0       0       0
## straw-its2-D10-4       0       0       0       2       2       2       2
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1183 Seq1184 Seq1185 Seq1186 Seq1187 Seq1188 Seq1189
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       2       2       2       0       0       0       0
## straw-its2-D10-5       0       0       0       2       2       2       0
## straw-its2-D12-1       0       0       0       0       0       0       2
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1190 Seq1191 Seq1192 Seq1193 Seq1194 Seq1195 Seq1196
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       2       2       2       2       2       2       2
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1197 Seq1198 Seq1199 Seq1200 Seq1201 Seq1202 Seq1203
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       2       2       2       2       2       2       2
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1204 Seq1205 Seq1206 Seq1207 Seq1208 Seq1209 Seq1210
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       2       2       2       2       0       0       0
## straw-its2-D12-2       0       0       0       0       2       2       2
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1211 Seq1212 Seq1213 Seq1214 Seq1215 Seq1216 Seq1217
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       2       2       2       0       0       0       0
## straw-its2-D12-3       0       0       0       2       2       2       2
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1218 Seq1219 Seq1220 Seq1221 Seq1222 Seq1223 Seq1224
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       2       2       2       2       2       2       2
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1225 Seq1226 Seq1227 Seq1228 Seq1229 Seq1230 Seq1231
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       2       2       0       0       0       0       0
## straw-its2-D13-2       0       0       2       2       2       2       2
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1232 Seq1233 Seq1234 Seq1235 Seq1236 Seq1237 Seq1238
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       2       2       2       2       2       2       0
## straw-its2-D13-3       0       0       0       0       0       0       2
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1239 Seq1240 Seq1241 Seq1242 Seq1243 Seq1244 Seq1245
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       2       0       0       0       0       0       0
## straw-its2-D14-1       0       2       2       2       2       2       2
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1246 Seq1247 Seq1248 Seq1249 Seq1250 Seq1251 Seq1252
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       2       0       0       0       0       0       0
## straw-its2-D14-2       0       2       2       2       2       2       2
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1253 Seq1254 Seq1255 Seq1256 Seq1257 Seq1258 Seq1259
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       2       2       2       2       2       0       0
## straw-its2-D14-3       0       0       0       0       0       2       2
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1260 Seq1261 Seq1262 Seq1263 Seq1264 Seq1265 Seq1266
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       2       2       2       0       0       0       0
## straw-its2-D14-4       0       0       0       2       2       2       2
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1267 Seq1268 Seq1269 Seq1270 Seq1271 Seq1272 Seq1273
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       2       2       0       0       0       0       0
## straw-its2-D14-5       0       0       2       2       2       2       2
## straw-its2-D15-1       0       0       0       0       0       0       0
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1274 Seq1275 Seq1276 Seq1277 Seq1278 Seq1279 Seq1280
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       2       0       0       0       0       0       0
## straw-its2-D15-1       0       2       2       2       2       2       2
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1281 Seq1282 Seq1283 Seq1284 Seq1285 Seq1286 Seq1287
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       2       2       2       2       2       2       2
## straw-its2-D15-2       0       0       0       0       0       0       0
## straw-its2-D15-3       0       0       0       0       0       0       0
##                  Seq1288 Seq1289 Seq1290 Seq1291 Seq1292 Seq1293 Seq1294
## straw-its2-D01-1       0       0       0       0       0       0       0
## straw-its2-D01-2       0       0       0       0       0       0       0
## straw-its2-D01-3       0       0       0       0       0       0       0
## straw-its2-D03-1       0       0       0       0       0       0       0
## straw-its2-D03-2       0       0       0       0       0       0       0
## straw-its2-D03-3       0       0       0       0       0       0       0
## straw-its2-D05-1       0       0       0       0       0       0       0
## straw-its2-D05-2       0       0       0       0       0       0       0
## straw-its2-D05-3       0       0       0       0       0       0       0
## straw-its2-D05-4       0       0       0       0       0       0       0
## straw-its2-D05-5       0       0       0       0       0       0       0
## straw-its2-D07-1       0       0       0       0       0       0       0
## straw-its2-D07-2       0       0       0       0       0       0       0
## straw-its2-D07-3       0       0       0       0       0       0       0
## straw-its2-D08-1       0       0       0       0       0       0       0
## straw-its2-D08-2       0       0       0       0       0       0       0
## straw-its2-D08-3       0       0       0       0       0       0       0
## straw-its2-D10-1       0       0       0       0       0       0       0
## straw-its2-D10-2       0       0       0       0       0       0       0
## straw-its2-D10-3       0       0       0       0       0       0       0
## straw-its2-D10-4       0       0       0       0       0       0       0
## straw-its2-D10-5       0       0       0       0       0       0       0
## straw-its2-D12-1       0       0       0       0       0       0       0
## straw-its2-D12-2       0       0       0       0       0       0       0
## straw-its2-D12-3       0       0       0       0       0       0       0
## straw-its2-D13-1       0       0       0       0       0       0       0
## straw-its2-D13-2       0       0       0       0       0       0       0
## straw-its2-D13-3       0       0       0       0       0       0       0
## straw-its2-D14-1       0       0       0       0       0       0       0
## straw-its2-D14-2       0       0       0       0       0       0       0
## straw-its2-D14-3       0       0       0       0       0       0       0
## straw-its2-D14-4       0       0       0       0       0       0       0
## straw-its2-D14-5       0       0       0       0       0       0       0
## straw-its2-D15-1       2       2       2       2       0       0       0
## straw-its2-D15-2       0       0       0       0       2       2       0
## straw-its2-D15-3       0       0       0       0       0       0       2
##                  Seq1295
## straw-its2-D01-1       0
## straw-its2-D01-2       0
## straw-its2-D01-3       0
## straw-its2-D03-1       0
## straw-its2-D03-2       0
## straw-its2-D03-3       0
## straw-its2-D05-1       0
## straw-its2-D05-2       0
## straw-its2-D05-3       0
## straw-its2-D05-4       0
## straw-its2-D05-5       0
## straw-its2-D07-1       0
## straw-its2-D07-2       0
## straw-its2-D07-3       0
## straw-its2-D08-1       0
## straw-its2-D08-2       0
## straw-its2-D08-3       0
## straw-its2-D10-1       0
## straw-its2-D10-2       0
## straw-its2-D10-3       0
## straw-its2-D10-4       0
## straw-its2-D10-5       0
## straw-its2-D12-1       0
## straw-its2-D12-2       0
## straw-its2-D12-3       0
## straw-its2-D13-1       0
## straw-its2-D13-2       0
## straw-its2-D13-3       0
## straw-its2-D14-1       0
## straw-its2-D14-2       0
## straw-its2-D14-3       0
## straw-its2-D14-4       0
## straw-its2-D14-5       0
## straw-its2-D15-1       0
## straw-its2-D15-2       0
## straw-its2-D15-3       2

Все its филотипы

amp_its
## ampvis2 object with 4 elements. 
## Summary of OTU table:
##      Samples         OTUs  Total#Reads    Min#Reads    Max#Reads Median#Reads 
##           36         1295       815134        13533        34994        22657 
##    Avg#Reads 
##     22642.61 
## 
## Assigned taxonomy:
##     Kingdom      Phylum       Class       Order      Family       Genus 
##    554(43%) 453(34.98%) 362(27.95%) 335(25.87%) 321(24.79%) 306(23.63%) 
##     Species 
## 207(15.98%) 
## 
## Metadata variables: 3 
##  SampleID, Day, Description

Филы ао всем

amp_heatmap(amp_its,
            tax_show = 7,
            group_by = "Day",
            tax_aggregate = "Phylum",
            tax_add = "Kingdom",
            normalise=TRUE,
            showRemainingTaxa = TRUE)
## Warning: Transformation introduced infinite values in discrete y-axis

Те, которые пойдут в WGCNA(116 филотипов)

amp_heatmap(amp_its_inall,
            tax_show = 40 ,
            group_by = "Day",
            tax_aggregate = "OTU",
            tax_add = "Genus",
            normalise=TRUE,
            showRemainingTaxa = TRUE)
## Warning: Transformation introduced infinite values in discrete y-axis

beta_custom_norm_NMDS_elli_w(ps_its, Group="Day", Color="Day")
## Square root transformation
## Wisconsin double standardization
## Run 0 stress 0.1834317 
## Run 1 stress 0.2171478 
## Run 2 stress 0.1841584 
## Run 3 stress 0.1841584 
## Run 4 stress 0.1834317 
## ... Procrustes: rmse 0.00001261231  max resid 0.00003592311 
## ... Similar to previous best
## Run 5 stress 0.1834317 
## ... New best solution
## ... Procrustes: rmse 0.0000323766  max resid 0.00007990469 
## ... Similar to previous best
## Run 6 stress 0.231872 
## Run 7 stress 0.1841584 
## Run 8 stress 0.1841585 
## Run 9 stress 0.1834317 
## ... New best solution
## ... Procrustes: rmse 0.00001517606  max resid 0.00006303215 
## ... Similar to previous best
## Run 10 stress 0.1841585 
## Run 11 stress 0.1834317 
## ... Procrustes: rmse 0.000038015  max resid 0.000121633 
## ... Similar to previous best
## Run 12 stress 0.1841584 
## Run 13 stress 0.1841584 
## Run 14 stress 0.1834318 
## ... Procrustes: rmse 0.00003306352  max resid 0.000165396 
## ... Similar to previous best
## Run 15 stress 0.1834317 
## ... Procrustes: rmse 0.00004440375  max resid 0.0001204561 
## ... Similar to previous best
## Run 16 stress 0.2231292 
## Run 17 stress 0.1834317 
## ... New best solution
## ... Procrustes: rmse 0.0000110403  max resid 0.0000307291 
## ... Similar to previous best
## Run 18 stress 0.1841584 
## Run 19 stress 0.2306513 
## Run 20 stress 0.1841584 
## *** Solution reached

otu.inall <- as.data.frame(ps.its.inall@otu_table@.Data) 
ps.inall.clr <- ps.its.inall
otu_table(ps.inall.clr) <- phyloseq::otu_table(compositions::clr(otu.inall), taxa_are_rows = FALSE)
data <- ps.inall.clr@otu_table@.Data %>% 
  as.data.frame()
rownames(data) <- as.character(ps.inall.clr@sam_data$Description)
powers <-  c(c(1:10), seq(from = 12, to=30, by=1))
sft <-  pickSoftThreshold(data, powerVector = powers, verbose = 5, networkType = "signed")
## pickSoftThreshold: will use block size 116.
##  pickSoftThreshold: calculating connectivity for given powers...
##    ..working on genes 1 through 116 of 116
##    Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
## 1      1   0.3860 -25.70         0.5550 57.2000 57.100000 59.600
## 2      2   0.4580 -17.60         0.3190 29.5000 29.300000 32.400
## 3      3   0.4860 -11.60         0.3420 15.8000 15.600000 18.500
## 4      4   0.6370  -7.48         0.5340  8.7100  8.530000 11.300
## 5      5   0.7900  -5.30         0.7300  4.9900  4.780000  7.370
## 6      6   0.8050  -3.89         0.7500  2.9600  2.770000  5.090
## 7      7   0.8400  -2.94         0.8030  1.8300  1.650000  3.710
## 8      8   0.7890  -2.65         0.7530  1.1700  1.000000  2.820
## 9      9   0.2080  -7.17        -0.0165  0.7790  0.626000  2.230
## 10    10   0.8000  -1.88         0.8250  0.5400  0.401000  1.810
## 11    12   0.8610  -1.51         0.9500  0.2890  0.173000  1.360
## 12    13   0.7990  -1.44         0.8150  0.2230  0.121000  1.220
## 13    14   0.8000  -1.34         0.8260  0.1770  0.083400  1.120
## 14    15   0.7480  -1.32         0.7690  0.1440  0.057500  1.020
## 15    16   0.1540  -2.22        -0.0813  0.1190  0.040100  0.941
## 16    17   0.1530  -2.10        -0.0816  0.1010  0.027800  0.869
## 17    18   0.8570  -1.15         0.8780  0.0866  0.019400  0.805
## 18    19   0.0897  -1.46        -0.0687  0.0754  0.013700  0.746
## 19    20   0.0930  -1.43        -0.0720  0.0663  0.009910  0.693
## 20    21   0.2140  -2.01         0.0509  0.0589  0.007180  0.660
## 21    22   0.2200  -2.04         0.0648  0.0527  0.005230  0.643
## 22    23   0.0951  -1.76        -0.0800  0.0475  0.003800  0.627
## 23    24   0.1930  -1.80        -0.0248  0.0431  0.002730  0.612
## 24    25   0.1960  -1.82        -0.0191  0.0393  0.001970  0.598
## 25    26   0.2010  -2.33        -0.0126  0.0360  0.001440  0.585
## 26    27   0.2220  -2.37         0.0609  0.0331  0.001070  0.572
## 27    28   0.2290  -2.40         0.0789  0.0305  0.000788  0.559
## 28    29   0.2320  -2.67         0.0387  0.0283  0.000584  0.547
## 29    30   0.2430  -2.73         0.0567  0.0263  0.000433  0.536
plot(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2], xlab="Soft Threshold (power)",ylab="Scale Free Topology Model Fit,signed R^2",type="n", main = paste("Scale independence"))
text(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2], labels=powers,cex=0.9,col="red")
abline(h=0.9,col="salmon")

ps.varstab <- ps_vst(ps.its.inall, "Day")

data2 <- ps.varstab@otu_table@.Data %>% 
  as.data.frame()

rownames(data2) <- as.character(ps.varstab@sam_data$Description)
powers <-  c(seq(from = 1, to=10, by=0.5), seq(from = 11, to=20, by=1))
sft2 <-  pickSoftThreshold(data2, powerVector = powers, verbose = 5, networkType = "signed hybrid")
## pickSoftThreshold: will use block size 116.
##  pickSoftThreshold: calculating connectivity for given powers...
##    ..working on genes 1 through 116 of 116
##    Power SFT.R.sq  slope truncated.R.sq mean.k.  median.k. max.k.
## 1    1.0    0.352 -1.180        0.82400 11.7000 11.1000000  21.40
## 2    1.5    0.511 -0.965        0.80800  6.4500  5.9700000  13.20
## 3    2.0    0.688 -1.020        0.82800  3.9000  3.3000000   9.04
## 4    2.5    0.787 -0.915        0.80900  2.5200  1.9300000   6.41
## 5    3.0    0.828 -0.797        0.78200  1.7200  1.1700000   4.69
## 6    3.5    0.807 -0.913        0.75900  1.2300  0.7570000   3.81
## 7    4.0    0.789 -1.110        0.73200  0.9160  0.5010000   3.54
## 8    4.5    0.200 -2.790        0.08170  0.7060  0.3370000   3.34
## 9    5.0    0.218 -2.720        0.11300  0.5610  0.2300000   3.18
## 10   5.5    0.235 -3.520        0.08280  0.4570  0.1590000   3.04
## 11   6.0    0.165 -2.140       -0.07370  0.3800  0.1100000   2.92
## 12   6.5    0.204 -2.250       -0.00278  0.3220  0.0758000   2.82
## 13   7.0    0.208 -2.210        0.00364  0.2780  0.0538000   2.73
## 14   7.5    0.192 -2.760       -0.03940  0.2430  0.0391000   2.65
## 15   8.0    0.192 -2.670       -0.03910  0.2150  0.0280000   2.57
## 16   8.5    0.196 -2.600       -0.03270  0.1920  0.0203000   2.50
## 17   9.0    0.228 -2.770        0.01890  0.1740  0.0148000   2.44
## 18   9.5    0.213 -2.990       -0.00815  0.1580  0.0108000   2.37
## 19  10.0    0.214 -3.060       -0.00549  0.1450  0.0078000   2.32
## 20  11.0    0.230 -3.170        0.01010  0.1240  0.0041500   2.21
## 21  12.0    0.262 -3.210        0.05580  0.1080  0.0024100   2.12
## 22  13.0    0.222 -3.130        0.01010  0.0955  0.0014200   2.03
## 23  14.0    0.234 -3.060        0.02160  0.0855  0.0008090   1.95
## 24  15.0    0.259 -3.140        0.04770  0.0774  0.0004490   1.88
## 25  16.0    0.270 -3.070        0.06090  0.0707  0.0002500   1.82
## 26  17.0    0.233 -2.840        0.04610  0.0651  0.0001400   1.76
## 27  18.0    0.244 -2.790        0.05240  0.0602  0.0000789   1.71
## 28  19.0    0.251 -2.860        0.06040  0.0561  0.0000444   1.66
## 29  20.0    0.280 -3.030        0.08580  0.0525  0.0000250   1.62
plot(sft2$fitIndices[,1], -sign(sft2$fitIndices[,3])*sft2$fitIndices[,2], xlab="Soft Threshold (power)",ylab="Scale Free Topology Model Fit,signed R^2",type="n", main = paste("Scale independence"))
text(sft2$fitIndices[,1], -sign(sft2$fitIndices[,3])*sft2$fitIndices[,2], labels=powers,cex=0.9,col="red")
abline(h=0.9,col="salmon")

# WGCNA, as old and not supported
detachAllPackages()
library(WGCNA)


net3 <- WGCNA::blockwiseModules(data2,
                          power=3,
                          TOMType="signed",
                          networkType="signed hybrid",
                          nThreads=0)


mergedColors2 <-  WGCNA::labels2colors(net3$colors, colorSeq = c("salmon", "darkgreen", "cyan", "red", "blue", "plum"))

plotDendroAndColors(
  net3$dendrograms[[1]],
  mergedColors2[net3$blockGenes[[1]]],
  "Module colors",
  dendroLabels = FALSE,
  hang = 0.03,
  addGuide = TRUE,
  guideHang = 0.05)

library(phyloseq)
library(tidyverse)
library(ggpubr)
library(ampvis2)
library(heatmaply)
library(WGCNA)
library(phyloseq)
library(ggtree)
library(tidyverse)
library(KneeArrower)

Зеленые - фон

modules_of_interest = mergedColors2 %>% 
  unique()

module_df <- data.frame(
  asv = names(net3$colors),
  colors = mergedColors2
)

# module_df[module_df == "yellow"] <- "salmon"

submod <-  module_df %>%
  subset(colors %in% modules_of_interest)

row.names(module_df) = module_df$asv

subexpr = as.data.frame(t(data2))[submod$asv,]

submod_df <- data.frame(subexpr) %>%
  mutate(
    asv = row.names(.)
  ) %>%
  pivot_longer(-asv) %>%
  mutate(
    module = module_df[asv,]$colors
  )

submod_df <- submod_df %>% 
  mutate(name = gsub("\\_.*","",submod_df$name)) %>% 
  group_by(name, asv) %>% 
  summarise(value = mean(value), asv = asv, module = module) %>% 
  relocate(c(asv, name, value, module)) %>% 
  ungroup() %>% 
  mutate(module = as.factor(module))

p <- submod_df %>% 
  ggplot(., aes(x=name, y=value, group=asv)) +
  geom_line(aes(color = module),
            alpha = 0.2) +
  theme_bw() +
  theme(
    axis.text.x = element_text(angle = 90),
    legend.position = "none") +
  facet_grid(rows = vars(module)) +
  labs(x = "treatment",
       y = "normalized expression")

p + scale_color_manual(values = levels(submod_df$module))

l_its <- color_filt_broken(ps_its, submod_df, ps.its.inall)
l_its

$cyan \(cyan\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 36 taxa and 36 samples ] sample_data() Sample Data: [ 36 samples by 2 sample variables ] tax_table() Taxonomy Table: [ 36 taxa by 7 taxonomic ranks ] refseq() DNAStringSet: [ 36 reference sequences ]

\(cyan\)amp ampvis2 object with 4 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 36 36 318660 0 23584 9007.5 Avg#Reads 8851.67

Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 28(78%) 25(69.44%) 17(47.22%) 12(33.33%) 12(33.33%) 12(33.33%) 9(25%)

Metadata variables: 3 SampleID, Day, Description

\(cyan\)heat \(cyan\)heat_rel \(cyan\)tree \(cyan\)taxa

Kingdom Phylum Class Order Family Genus Species
Seq1 k__Fungi p__Ascomycota c__Sordariomycetes o__Chaetosphaeriales f__Chaetosphaeriaceae g__Chloridium s__aseptatum
Seq2 k__Fungi p__Ascomycota c__Sordariomycetes o__Coniochaetales f__Coniochaetaceae g__Coniochaeta s__verticillata
Seq12 k__Fungi p__Ascomycota c__Sordariomycetes NA NA NA NA
Seq184 NA NA NA NA NA NA NA
Seq10 k__Fungi p__Ascomycota c__Sordariomycetes o__Coniochaetales f__Coniochaetaceae g__Coniochaeta s__canina
Seq73 k__Alveolata NA NA NA NA NA NA
Seq5 k__Fungi p__Ascomycota c__Sordariomycetes o__Coniochaetales f__Coniochaetaceae g__Coniochaeta s__verticillata
Seq118 k__Metazoa p__Nematoda NA NA NA NA NA
Seq18 k__Fungi p__Ascomycota c__Sordariomycetes NA NA NA NA
Seq93 k__Fungi p__Ascomycota c__Dothideomycetes o__Venturiales f__Sympoventuriaceae g__Scolecobasidium s__constrictum
Seq78 k__Metazoa p__Nematoda NA NA NA NA NA
Seq101 NA NA NA NA NA NA NA
Seq4 k__Fungi p__Ascomycota c__Sordariomycetes o__Coniochaetales f__Coniochaetaceae g__Coniochaeta s__verticillata
Seq62 k__Metazoa p__Nematoda NA NA NA NA NA
Seq48 k__Metazoa p__Nematoda NA NA NA NA NA
Seq36 k__Fungi p__Ascomycota c__Sordariomycetes NA NA NA NA
Seq44 k__Metazoa p__Nematoda NA NA NA NA NA
Seq103 k__Metazoa p__Nematoda NA NA NA NA NA
Seq166 k__Fungi p__Ascomycota c__Eurotiomycetes o__Chaetothyriales f__Herpotrichiellaceae g__Exophiala NA
Seq231 k__Eukaryota_kgd_Incertae_sedis NA NA NA NA NA NA
Seq21 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Clavicipitaceae g__Metarhizium s__marquandii
Seq108 k__Metazoa p__Nematoda NA NA NA NA NA
Seq74 k__Fungi p__Ascomycota c__Sordariomycetes NA NA NA NA
Seq195 NA NA NA NA NA NA NA
Seq28 k__Fungi p__Ascomycota c__Leotiomycetes o__Helotiales f__Helotiaceae g__Scytalidium NA
Seq104 k__Metazoa p__Nematoda c__Chromadorea o__Rhabditida f__Cephalobidae g__Pseudacrobeles NA
Seq29 k__Fungi p__Ascomycota c__Sordariomycetes o__Glomerellales f__Glomerellaceae g__Colletotrichum s__sidae
Seq46 k__Fungi p__Ascomycota c__Sordariomycetes NA NA NA NA
Seq122 NA NA NA NA NA NA NA
Seq235 NA NA NA NA NA NA NA
Seq191 NA NA NA NA NA NA NA
Seq94 k__Alveolata NA NA NA NA NA NA
Seq76 k__Fungi p__Ascomycota c__Sordariomycetes o__Sordariales f__Sordariales_fam_Incertae_sedis g__Staphylotrichum s__boninense
Seq155 NA NA NA NA NA NA NA
Seq190 NA NA NA NA NA NA NA
Seq32 k__Metazoa p__Nematoda NA NA NA NA NA

$darkgreen \(darkgreen\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 56 taxa and 36 samples ] sample_data() Sample Data: [ 36 samples by 2 sample variables ] tax_table() Taxonomy Table: [ 56 taxa by 7 taxonomic ranks ] refseq() DNAStringSet: [ 56 reference sequences ]

\(darkgreen\)amp ampvis2 object with 4 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 36 56 261584 1790 20315 6577 Avg#Reads 7266.22

Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 52(93%) 51(91.07%) 48(85.71%) 48(85.71%) 48(85.71%) 48(85.71%) 34(60.71%)

Metadata variables: 3 SampleID, Day, Description

\(darkgreen\)heat \(darkgreen\)heat_rel \(darkgreen\)tree \(darkgreen\)taxa

Kingdom Phylum Class Order Family Genus Species
Seq92 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Bolbitiaceae g__Conocybe s__zeylanica
Seq49 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Bolbitiaceae g__Conocybe s__zeylanica
Seq91 k__Fungi p__Ascomycota c__Sordariomycetes o__Coniochaetales f__Coniochaetaceae g__Coniochaeta s__canina
Seq6 k__Fungi p__Ascomycota c__Sordariomycetes o__Sordariales f__Chaetomiaceae g__Humicola s__sardiniae
Seq16 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Bolbitiaceae g__Conocybe s__zeylanica
Seq67 k__Metazoa p__Annelida c__Clitellata o__Enchytraeida f__Enchytraeidae g__Fridericia NA
Seq13 k__Fungi p__Ascomycota c__Eurotiomycetes o__Eurotiales f__Trichocomaceae g__Talaromyces NA
Seq7 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Bolbitiaceae g__Conocybe s__zeylanica
Seq25 k__Fungi p__Basidiomycota c__Cystobasidiomycetes o__Cystobasidiales f__Cystobasidiaceae g__Occultifur NA
Seq69 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Nectriaceae g__Gibberella s__intricans
Seq86 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Bolbitiaceae g__Conocybe s__zeylanica
Seq205 k__Fungi p__Mucoromycota c__Mucoromycetes o__Mucorales f__Rhizopodaceae g__Rhizopus s__arrhizus
Seq50 k__Fungi p__Basidiomycota c__Cystobasidiomycetes o__Cystobasidiales f__Cystobasidiaceae g__Occultifur NA
Seq193 k__Heterolobosa p__Heterolobosa_phy_Incertae_sedis c__Heterolobosea o__Schizopyrenida f__Vahlkampfiidae g__Naegleria NA
Seq136 k__Fungi p__Ascomycota c__Eurotiomycetes o__Chaetothyriales f__Herpotrichiellaceae g__Exophiala NA
Seq23 k__Fungi p__Mucoromycota c__Mucoromycetes o__Mucorales f__Mucoraceae g__Actinomucor s__elegans
Seq175 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Bionectriaceae g__Clonostachys s__rosea
Seq281 k__Heterolobosa p__Heterolobosa_phy_Incertae_sedis c__Heterolobosea o__Schizopyrenida f__Vahlkampfiidae g__Allovahlkampfia NA
Seq47 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Nectriaceae g__Gibberella s__intricans
Seq137 k__Fungi p__Ascomycota c__Dothideomycetes o__Venturiales f__Sympoventuriaceae g__Ochroconis s__tshawytschae
Seq9 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Stachybotryaceae g__Albifimbria s__verrucaria
Seq42 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Bolbitiaceae g__Conocybe s__zeylanica
Seq45 k__Fungi NA NA NA NA NA NA
Seq11 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Nectriaceae g__Gibberella s__intricans
Seq89 k__Fungi p__Basidiomycota c__Cystobasidiomycetes o__Cystobasidiales f__Cystobasidiaceae g__Occultifur NA
Seq171 k__Fungi p__Ascomycota c__Dothideomycetes o__Venturiales f__Sympoventuriaceae g__Ochroconis s__tshawytschae
Seq178 k__Fungi p__Ascomycota c__Dothideomycetes o__Venturiales f__Sympoventuriaceae g__Scolecobasidium s__constrictum
Seq22 k__Fungi p__Ascomycota c__Sordariomycetes o__Coniochaetales f__Coniochaetaceae g__Coniochaeta s__verticillata
Seq31 k__Fungi p__Mucoromycota c__Mucoromycetes o__Mucorales f__Mucoraceae g__Actinomucor s__elegans
Seq65 k__Fungi p__Ascomycota c__Sordariomycetes o__Coniochaetales f__Coniochaetaceae g__Coniochaeta NA
Seq75 NA NA NA NA NA NA NA
Seq85 k__Metazoa p__Nematoda NA NA NA NA NA
Seq54 k__Fungi p__Ascomycota c__Sordariomycetes o__Coniochaetales f__Coniochaetaceae g__Coniochaeta NA
Seq121 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Nectriaceae g__Gibberella s__intricans
Seq125 k__Fungi p__Ascomycota c__Dothideomycetes o__Venturiales f__Sympoventuriaceae g__Ochroconis s__tshawytschae
Seq181 k__Fungi p__Ascomycota c__Eurotiomycetes o__Eurotiales f__Aspergillaceae g__Penicillium s__bialowiezense
Seq24 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Nectriaceae g__Gibberella s__intricans
Seq27 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Stachybotryaceae g__Stachybotrys s__chartarum
Seq66 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Stachybotryaceae g__Albifimbria s__verrucaria
Seq114 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Bolbitiaceae g__Conocybe s__zeylanica
Seq15 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Nectriaceae g__Gibberella s__intricans
Seq226 k__Fungi p__Ascomycota c__Dothideomycetes o__Venturiales f__Sympoventuriaceae g__Scolecobasidium s__constrictum
Seq26 k__Fungi p__Ascomycota c__Sordariomycetes o__Sordariales f__Chaetomiaceae g__Chaetomium s__iranianum
Seq59 k__Fungi p__Ascomycota c__Dothideomycetes o__Venturiales f__Sympoventuriaceae g__Ochroconis s__tshawytschae
Seq41 k__Fungi p__Basidiomycota c__Agaricomycetes o__Cantharellales f__Ceratobasidiaceae g__Waitea s__circinata
Seq157 k__Fungi p__Ascomycota c__Sordariomycetes o__Sordariales f__Chaetomiaceae g__Zopfiella NA
Seq124 k__Fungi p__Ascomycota c__Eurotiomycetes o__Eurotiales f__Aspergillaceae g__Aspergillus NA
Seq254 k__Metazoa p__Nematoda NA NA NA NA NA
Seq17 k__Metazoa p__Nematoda NA NA NA NA NA
Seq39 k__Fungi p__Ascomycota c__Sordariomycetes o__Coniochaetales f__Coniochaetaceae g__Coniochaeta s__verticillata
Seq180 NA NA NA NA NA NA NA
Seq20 k__Fungi p__Ascomycota c__Sordariomycetes o__Sordariales f__Chaetomiaceae g__Chaetomium NA
Seq102 NA NA NA NA NA NA NA
Seq70 k__Fungi p__Ascomycota c__Sordariomycetes o__Sordariales f__Sordariales_fam_Incertae_sedis g__Staphylotrichum s__boninense
Seq150 k__Heterolobosa p__Heterolobosa_phy_Incertae_sedis c__Heterolobosea o__Schizopyrenida f__Vahlkampfiidae g__Allovahlkampfia NA
Seq132 NA NA NA NA NA NA NA

$salmon \(salmon\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 24 taxa and 36 samples ] sample_data() Sample Data: [ 36 samples by 2 sample variables ] tax_table() Taxonomy Table: [ 24 taxa by 7 taxonomic ranks ] refseq() DNAStringSet: [ 24 reference sequences ]

\(salmon\)amp ampvis2 object with 4 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 36 24 121335 20 14955 1772 Avg#Reads 3370.42

Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 22(92%) 18(75%) 15(62.5%) 14(58.33%) 13(54.17%) 13(54.17%) 11(45.83%)

Metadata variables: 3 SampleID, Day, Description

\(salmon\)heat \(salmon\)heat_rel \(salmon\)tree \(salmon\)taxa

Kingdom Phylum Class Order Family Genus Species
Seq3 k__Fungi p__Ascomycota c__Sordariomycetes o__Sordariales f__Lasiosphaeriaceae g__Schizothecium s__inaequale
Seq19 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Psathyrellaceae g__Coprinellus s__flocculosus
Seq53 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Stachybotryaceae g__Albifimbria s__verrucaria
Seq99 k__Viridiplantae p__Anthophyta NA NA NA NA NA
Seq215 k__Viridiplantae NA NA NA NA NA NA
Seq30 k__Fungi p__Ascomycota c__Sordariomycetes o__Sordariales f__Chaetomiaceae g__Humicola s__sardiniae
Seq43 k__Fungi p__Ascomycota c__Sordariomycetes o__Sordariales f__Lasiosphaeriaceae g__Schizothecium NA
Seq68 NA NA NA NA NA NA NA
Seq63 k__Fungi p__Mucoromycota c__Mucoromycetes o__Mucorales f__Mucoraceae g__Actinomucor s__elegans
Seq100 k__Fungi NA NA NA NA NA NA
Seq140 k__Fungi p__Ascomycota c__Dothideomycetes o__Pleosporales NA NA NA
Seq33 k__Fungi p__Basidiomycota c__Agaricomycetes o__Agaricales f__Psathyrellaceae g__Coprinellus s__flocculosus
Seq245 NA NA NA NA NA NA NA
Seq138 k__Viridiplantae p__Anthophyta c__Eudicotyledonae NA NA NA NA
Seq8 k__Fungi p__Ascomycota c__Sordariomycetes o__Sordariales f__Lasiosphaeriaceae g__Schizothecium s__inaequale
Seq79 k__Viridiplantae p__Anthophyta NA NA NA NA NA
Seq161 k__Eukaryota_kgd_Incertae_sedis NA NA NA NA NA NA
Seq96 k__Metazoa p__Nematoda c__Chromadorea o__Rhabditida f__Cephalobidae g__Acrobeloides s__nanus
Seq147 k__Fungi NA NA NA NA NA NA
Seq123 k__Fungi p__Ascomycota c__Sordariomycetes o__Sordariales f__Chaetomiaceae g__Chaetomium s__jodhpurense
Seq152 k__Viridiplantae p__Anthophyta NA NA NA NA NA
Seq52 k__Fungi p__Ascomycota c__Sordariomycetes o__Sordariales f__Lasiosphaeriaceae g__Schizothecium NA
Seq40 k__Fungi p__Mucoromycota c__Mucoromycetes o__Mucorales f__Mucoraceae g__Actinomucor s__elegans
Seq37 k__Fungi p__Ascomycota c__Sordariomycetes o__Hypocreales f__Nectriaceae g__Gibberella s__intricans
sample.data <- ps_its@sam_data %>% 
  data.frame() %>% 
  mutate(Group = if_else(Day %in% c("D01", "D03", "D05"), "early", 
                         if_else(Day %in% c("D07", "D08","D10"), "middle", "late"))) %>% 
  mutate(Group = factor(Group, levels=c("early", "middle","late"))) %>% 
  phyloseq::sample_data()

sample_data(ps_its) <- sample.data

p.observed <- plot_alpha_w_toc(ps = ps_its, group = "Group", metric = c("Observed")) + 
  theme(axis.title.y = element_blank())

p.shannon <- plot_alpha_w_toc(ps = ps_its, group = "Group", metric = c("Shannon")) + 
  theme(axis.title.y = element_blank())

p.simpson <- plot_alpha_w_toc(ps = ps_its, group = "Group", metric = c("InvSimpson")) + 
  theme(axis.title.y = element_blank())

ggpubr::ggarrange(p.observed, p.shannon, p.simpson, ncol = 3)

p.observed <- plot_alpha_w_toc(ps = ps_its, group = "Day", metric = c("Observed")) + 
  theme(axis.title.y = element_blank())

p.shannon <- plot_alpha_w_toc(ps = ps_its, group = "Day", metric = c("Shannon")) + 
  theme(axis.title.y = element_blank())

p.simpson <- plot_alpha_w_toc(ps = ps_its, group = "Day", metric = c("InvSimpson")) + 
  theme(axis.title.y = element_blank())

ggpubr::ggarrange(p.observed, p.shannon, p.simpson, ncol = 3)

ps.m <- phyloseq::psmelt(ps_its)
ps.m <- ps.m %>% 
  mutate_if(is.character, as.factor) 

ps.data.out <- ps.m %>%
  select(-Group) %>% 
  pivot_wider(names_from = c(Day, Description, Sample), values_from = Abundance, values_fill = 0) 

#create empty dataframe with columnnames
external_empty_dataframe <- data.frame(OTU=factor(), cluster=factor(), stringsAsFactors = FALSE)

for (i in names(l_its)) {
  a <- taxa_names(l_its[[i]][["ps"]])
  b <- rep(i, length(a))
  d <- data.frame(OTU = as.factor(a),
                  cluster = as.factor(b))
  external_empty_dataframe <- rbind(external_empty_dataframe, d)
}

clusters.otu.df <- external_empty_dataframe
# add exl taxa -- taxa "exl"
d <- data.frame(OTU = as.factor(ps.its.exl.taxa),
                cluster = as.factor(rep("exl", length(ps.its.exl.taxa))))

clusters.otu.df <- rbind(clusters.otu.df, d)
ps.data.out.exl <- left_join(clusters.otu.df, ps.data.out, by="OTU")
# write.table(ps.data.out.exl, file = "ps.its.data.out.tsv", sep = "\t")


ps.data.out.exl